rs2957127

Variant names:

• chr18-62392132-T-C
• rs2957127

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.557 in 151,598 control chromosomes in the GnomAD database, including 24,215 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24215 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84470 AN: 151480 Hom.: 24209 Cov.: 29

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.592

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.557 AC: 84509 AN: 151598 Hom.: 24215 Cov.: 29 AF XY: 0.548 AC XY: 40580 AN XY: 74068

African (AFR) AF: 0.602 AC: 24857 AN: 41294

American (AMR) AF: 0.543 AC: 8273 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2112 AN: 3464

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2702 AN: 4788

European-Finnish (FIN) AF: 0.417 AC: 4361 AN: 10454

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38982 AN: 67900

Other (OTH) AF: 0.589 AC: 1234 AN: 2094

Alfa AF: 0.544 Hom.: 3010

Bravo AF: 0.567

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.82
PhyloP100		0.031

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2957127; hg19: chr18-60059365;