17-7634474-T-C

Variant names:

• chr17-7634474-T-C
• rs727428

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 0.545 in 151,992 control chromosomes in the GnomAD database, including 22,908 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 0.54 (22908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 85 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82774 AN: 151874 Hom.: 22900 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.545 AC: 82808 AN: 151992 Hom.: 22908 Cov.: 31 AF XY: 0.545 AC XY: 40484 AN XY: 74290

African (AFR) AF: 0.480 AC: 19909 AN: 41470

American (AMR) AF: 0.611 AC: 9318 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2581 AN: 5146

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4814

European-Finnish (FIN) AF: 0.625 AC: 6604 AN: 10574

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38898 AN: 67962

Other (OTH) AF: 0.566 AC: 1192 AN: 2106

Alfa AF: 0.562 Hom.: 95274

Bravo AF: 0.543

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs727428; hg19: chr17-7537792; COSMIC: COSV61411358;