5-161723470-C-T

Variant names:

• chr5-161723470-C-T
• rs7713215

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.629 AC: 26079 AN: 41434

American (AMR) AF: 0.699 AC: 10679 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3462

East Asian (EAS) AF: 0.753 AC: 3883 AN: 5154

South Asian (SAS) AF: 0.695 AC: 3349 AN: 4816

European-Finnish (FIN) AF: 0.640 AC: 6736 AN: 10528

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41651 AN: 67918

Other (OTH) AF: 0.643 AC: 1354 AN: 2106

Alfa AF: 0.626 Hom.: 3875

Bravo AF: 0.640

Asia WGS AF: 0.748 AC: 2602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.39
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7713215; hg19: chr5-161150476;