17-7642666-T-C

Variant names:

• chr17-7642666-T-C
• rs1641536

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 152,106 control chromosomes in the GnomAD database, including 45,361 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 (45361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.757 AC: 115006 AN: 151988 Hom.: 45362 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.756 AC: 115049 AN: 152106 Hom.: 45361 Cov.: 32 AF XY: 0.755 AC XY: 56161 AN XY: 74344

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.793

Alfa AF: 0.813 Hom.: 6366

Bravo AF: 0.744

Asia WGS AF: 0.709 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1641536; hg19: chr17-7545984;