Is CORO7 c.2772+50C>T pathogenic?

CORO7 c.2772+50C>T is classified Uncertain significance in CORO7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2015-10-22). Absent from gnomAD v4.1; Associated with acute megakaryoblastic leukemia.

What condition is associated with CORO7 c.2772+50C>T?

CORO7 c.2772+50C>T is associated with acute megakaryoblastic leukemia, mediastinal germ cell tumor (ClinVar).

How common is CORO7 c.2772+50C>T in the general population?

CORO7 c.2772+50C>T is absent from gnomAD v4.1 (gnomAD).

How is Acute megakaryoblastic leukemia inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

CORO7 c.2772+50C>T

rs1555468179 · VCV218341

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

acute megakaryoblastic leukemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +50	near-intronic (+50 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -2.3
Non-coding constraint	Z 1.75	1 kb window · o/e 0.89 · regional · uncalibrated
Overall
CADD	0.159	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CORO7
Coding: c.2772+50C>T
MANE Select: NM_024535
dbSNP: rs1555468179
Type: single nucleotide variant
Location: chr16:4355236 (GRCh38)
Gene constraint: LOEUF 1.089 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.71 · 1 PDB

Full CORO7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

acute megakaryoblastic leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: mediastinal germ cell tumor

For Acute megakaryoblastic leukemia (Orphanet):

Inheritance: Not applicable
Onset: Adult, Childhood
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

CORO7-PAM16 p.Arg193Gln Benign ★★ ⚠ same type
CORO7 p.Arg601His Uncertain significance ★ ⚠ same type
CORO7 p.Asp50Asn Uncertain significance ★ ⚠ same type
CORO7 p.Lys151Thr Uncertain significance ★ ⚠ same type
CORO7 p.Val322Ile Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Ala403Val Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Arg559Cys Uncertain significance ★ ⚠ same type
CORO7-PAM16 p.Arg876Trp Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/coro7-c-2772-plus-50c-t (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown