Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.39%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -5.1 |
| Overall | ||
| CADD | 8.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.39%
European (non-Finnish) · 16,368/1,176,924 alleles
Filtering AF
1.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.37%
Overall
1.09%
17,590/1,610,326 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.39% | 72 |
| Remaining individualsnot grpmax-eligible | 0.845% | 118 |
| Ashkenazi Jewishnot grpmax-eligible | 0.443% | 226 |
| Finnishnot grpmax-eligible | 0.311% | 321 |
| Admixed American | 0.294% | 340 |
| African / African-American | 0.187% | 535 |
| Middle Eastern | 0.116% | 865 |
| South Asian | 0.0462% | 2,165 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PAM
- Protein
- p.Pro350=
- Coding
- c.1050C>T
- MANE Select
- NM_015057 · reported on NM_001177306
- dbSNP
- rs2217252
- Type
- single nucleotide variant
- Location
- chr5:102960019 (GRCh38)
Similar variants
- MYCBP2 p.Asp4042Val Uncertain significance ★★ same type
- MYCBP2 p.Asp4087Asn Uncertain significance ★★ same type
- MYCBP2 p.Gly877Ala Uncertain significance ★★ ⚠ same type
- MYCBP2 p.His2087Leu Uncertain significance ★★ ⚠ same type
- MYCBP2 p.Leu3349Phe Uncertain significance ★★ ⚠ same type
- MYCBP2 p.Lys2309Ter Uncertain significance ★★ same type
- MYCBP2 p.Phe1319Leu Uncertain significance ★★ same type
- MYCBP2 p.Tyr962Cys 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/pam-p-pro350 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown