chr17-71403132-T-C

Variant names:

• chr17-71403132-T-C
• rs917344

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 0.937 in 152,238 control chromosomes in the GnomAD database, including 67,395 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 0.94 (67395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 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: 0.937 AC: 142479 AN: 152120 Hom.: 67332 Cov.: 32

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.937 AC: 142603 AN: 152238 Hom.: 67395 Cov.: 32 AF XY: 0.932 AC XY: 69351 AN XY: 74422

African (AFR) AF: 0.976 AC: 40536 AN: 41542

American (AMR) AF: 0.912 AC: 13956 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3351 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2489 AN: 5156

South Asian (SAS) AF: 0.825 AC: 3969 AN: 4808

European-Finnish (FIN) AF: 0.956 AC: 10141 AN: 10610

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65046 AN: 68030

Other (OTH) AF: 0.936 AC: 1979 AN: 2114

Alfa AF: 0.948 Hom.: 47060

Bravo AF: 0.935

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.071
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs917344; hg19: chr17-69399273;