8-17424902-T-C

Variant names:

• chr8-17424902-T-C
• rs13271465

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 0.722 in 152,112 control chromosomes in the GnomAD database, including 41,798 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 0.72 (41798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109761 AN: 151994 Hom.: 41805 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.722 AC: 109781 AN: 152112 Hom.: 41798 Cov.: 32 AF XY: 0.721 AC XY: 53623 AN XY: 74360

African (AFR) AF: 0.481 AC: 19939 AN: 41446

American (AMR) AF: 0.786 AC: 12019 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2733 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2558 AN: 5156

South Asian (SAS) AF: 0.765 AC: 3684 AN: 4816

European-Finnish (FIN) AF: 0.814 AC: 8624 AN: 10600

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.848 AC: 57683 AN: 68012

Other (OTH) AF: 0.728 AC: 1539 AN: 2114

Alfa AF: 0.796 Hom.: 155721

Bravo AF: 0.705

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs13271465; hg19: chr8-17282411;