rs807629

Variant names:

• chr2-15637305-G-A
• rs807629

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.744 in 152,046 control chromosomes in the GnomAD database, including 43,265 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 0.74 (43265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.744 AC: 112991 AN: 151928 Hom.: 43213 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.744 AC: 113105 AN: 152046 Hom.: 43265 Cov.: 32 AF XY: 0.743 AC XY: 55188 AN XY: 74292

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.705

Alfa AF: 0.697 Hom.: 4857

Bravo AF: 0.763

Asia WGS AF: 0.915 AC: 3180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807629; hg19: chr2-15777429;