chr17-7642815-T-C

Variant names:

• chr17-7642815-T-C
• rs1641535

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 0.756 in 152,176 control chromosomes in the GnomAD database, including 45,338 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 0.76 (45338 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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: 0.756 AC: 114974 AN: 152058 Hom.: 45340 Cov.: 34

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.756 AC: 115012 AN: 152176 Hom.: 45338 Cov.: 34 AF XY: 0.755 AC XY: 56156 AN XY: 74388

African (AFR) AF: 0.517 AC: 21440 AN: 41500

American (AMR) AF: 0.803 AC: 12265 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3385 AN: 5180

South Asian (SAS) AF: 0.806 AC: 3889 AN: 4824

European-Finnish (FIN) AF: 0.809 AC: 8567 AN: 10588

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59735 AN: 68014

Other (OTH) AF: 0.792 AC: 1673 AN: 2112

Alfa AF: 0.841 Hom.: 69268

Bravo AF: 0.744

Asia WGS AF: 0.708 AC: 2460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1641535; hg19: chr17-7546133;