rs7713215

Positions:

• chr5-161723470-C-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 0.635 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;