17-7636548-T-C

Variant names:

• chr17-7636548-T-C
• rs1641544

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.866 in 151,922 control chromosomes in the GnomAD database, including 58,317 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 (58317 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.866 AC: 131422 AN: 151804 Hom.: 58275 Cov.: 29

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.866 AC: 131516 AN: 151922 Hom.: 58317 Cov.: 29 AF XY: 0.871 AC XY: 64649 AN XY: 74244

African (AFR) AF: 0.645 AC: 26669 AN: 41346

American (AMR) AF: 0.936 AC: 14280 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3276 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5138 AN: 5148

South Asian (SAS) AF: 0.952 AC: 4581 AN: 4810

European-Finnish (FIN) AF: 0.942 AC: 9977 AN: 10590

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64609 AN: 67994

Other (OTH) AF: 0.886 AC: 1867 AN: 2108

Alfa AF: 0.911 Hom.: 69480

Bravo AF: 0.855

Asia WGS AF: 0.965 AC: 3354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs1641544; hg19: chr17-7539866;