17-7642403-T-C

Variant names:

• chr17-7642403-T-C
• rs1641537

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 151,948 control chromosomes in the GnomAD database, including 45,275 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 (45275 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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: 0.756 AC: 114814 AN: 151830 Hom.: 45276 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.653

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: 114855 AN: 151948 Hom.: 45275 Cov.: 30 AF XY: 0.755 AC XY: 56064 AN XY: 74250

African (AFR) AF: 0.517 AC: 21392 AN: 41402

American (AMR) AF: 0.803 AC: 12248 AN: 15258

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

East Asian (EAS) AF: 0.652 AC: 3369 AN: 5164

South Asian (SAS) AF: 0.806 AC: 3875 AN: 4810

European-Finnish (FIN) AF: 0.809 AC: 8544 AN: 10558

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

European-Non Finnish (NFE) AF: 0.878 AC: 59708 AN: 67980

Other (OTH) AF: 0.792 AC: 1664 AN: 2100

Alfa AF: 0.792 Hom.: 31365

Bravo AF: 0.744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.94
DANN	Benign	0.31
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1641537; hg19: chr17-7545721;