rs7713215

Variant names:

• chr5-161723470-C-T
• rs7713215

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 0.635 in 151,888 control chromosomes in the GnomAD database, including 30,774 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 (30774 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.635 AC: 96341 AN: 151770 Hom.: 30730 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.635 AC: 96438 AN: 151888 Hom.: 30774 Cov.: 31 AF XY: 0.639 AC XY: 47427 AN XY: 74226

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.643

Alfa AF: 0.625 Hom.: 3718

Bravo AF: 0.640

Asia WGS AF: 0.748 AC: 2602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7713215; hg19: chr5-161150476;