17-8662038-T-C

Variant names:

• chr17-8662038-T-C
• rs6503137

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 0.874 in 152,220 control chromosomes in the GnomAD database, including 58,202 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 0.87 (58202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132864 AN: 152102 Hom.: 58146 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.874 AC: 132975 AN: 152220 Hom.: 58202 Cov.: 31 AF XY: 0.871 AC XY: 64826 AN XY: 74420

African (AFR) AF: 0.922 AC: 38319 AN: 41548

American (AMR) AF: 0.879 AC: 13440 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3026 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4323 AN: 5186

South Asian (SAS) AF: 0.838 AC: 4041 AN: 4820

European-Finnish (FIN) AF: 0.843 AC: 8928 AN: 10588

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58169 AN: 67994

Other (OTH) AF: 0.861 AC: 1821 AN: 2114

Alfa AF: 0.862 Hom.: 246103

Bravo AF: 0.879

Asia WGS AF: 0.822 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.6
DANN	Benign	0.85
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6503137; hg19: chr17-8565356;