5-156971158-G-C

Variant names:

• chr5-156971158-G-C
• rs1501908

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 0.574 in 152,018 control chromosomes in the GnomAD database, including 26,311 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 0.57 (26311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 65 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87164 AN: 151900 Hom.: 26295 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.574 AC: 87208 AN: 152018 Hom.: 26311 Cov.: 32 AF XY: 0.582 AC XY: 43219 AN XY: 74316

African (AFR) AF: 0.372 AC: 15415 AN: 41428

American (AMR) AF: 0.687 AC: 10490 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3853 AN: 5174

South Asian (SAS) AF: 0.688 AC: 3317 AN: 4818

European-Finnish (FIN) AF: 0.685 AC: 7236 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42640 AN: 67968

Other (OTH) AF: 0.587 AC: 1238 AN: 2108

Alfa AF: 0.607 Hom.: 14256

Bravo AF: 0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.30
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1501908; hg19: chr5-156398169; COSMIC: COSV55997018;