17-7642815-T-C

Position:

• chr17-7642815-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.792

Alfa AF: 0.856 Hom.: 54612

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1641535; hg19: chr17-7546133;