17-71261692-G-A

Variant names:

• chr17-71261692-G-A
• rs2158906

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 0.628 in 151,996 control chromosomes in the GnomAD database, including 32,980 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 (32980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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: 0.628 AC: 95414 AN: 151880 Hom.: 32969 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.628 AC: 95444 AN: 151996 Hom.: 32980 Cov.: 32 AF XY: 0.633 AC XY: 47043 AN XY: 74280

African (AFR) AF: 0.313 AC: 12973 AN: 41444

American (AMR) AF: 0.682 AC: 10401 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2491 AN: 3464

East Asian (EAS) AF: 0.632 AC: 3258 AN: 5156

South Asian (SAS) AF: 0.771 AC: 3717 AN: 4818

European-Finnish (FIN) AF: 0.822 AC: 8689 AN: 10576

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51581 AN: 67966

Other (OTH) AF: 0.638 AC: 1348 AN: 2112

Alfa AF: 0.720 Hom.: 169502

Bravo AF: 0.601

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2158906; hg19: chr17-69257833;