rs7601713

chr2-156696348-A-Cchr2-156696348-A-Gchr2-156696348-A-T

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 0.782 in 152,172 control chromosomes in the GnomAD database, including 46,791 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 0.78 (46791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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 (AFR) allele frequency at 95% confidence interval = 0.843 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: 0.782 AC: 118890 AN: 152054 Hom.: 46731 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.782 AC: 119005 AN: 152172 Hom.: 46791 Cov.: 32 AF XY: 0.786 AC XY: 58481 AN XY: 74402

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.772

Alfa AF: 0.745 Hom.: 91671

Bravo AF: 0.787

Asia WGS AF: 0.816 AC: 2840 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	0.18
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7601713; hg19: chr2-157552860;