rs2036657

chr17-4721864-G-Achr17-4721864-G-C

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 0.63 in 152,104 control chromosomes in the GnomAD database, including 31,362 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 0.63 (31362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95697 AN: 151986 Hom.: 31334 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.630 AC: 95758 AN: 152104 Hom.: 31362 Cov.: 32 AF XY: 0.638 AC XY: 47414 AN XY: 74362

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.619

Alfa AF: 0.665 Hom.: 6997

Bravo AF: 0.613

Asia WGS AF: 0.794 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	6.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036657; hg19: chr17-4625159;