rs17195476

Variant names:

• chr13-72197263-C-A
• rs17195476

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0352 in 152,168 control chromosomes in the GnomAD database, including 128 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 0.035 (128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0352 (5354/152168) while in subpopulation AMR AF = 0.0496 (758/15278). AF 95% confidence interval is 0.0467. There are 128 homozygotes in GnomAd4. There are 2592 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 128 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5357 AN: 152052 Hom.: 128 Cov.: 32

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0673

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0352 AC: 5354 AN: 152168 Hom.: 128 Cov.: 32 AF XY: 0.0348 AC XY: 2592 AN XY: 74392

African (AFR) AF: 0.0195 AC: 811 AN: 41532

American (AMR) AF: 0.0496 AC: 758 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0730 AC: 253 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4824

European-Finnish (FIN) AF: 0.0324 AC: 343 AN: 10584

Middle Eastern (MID) AF: 0.0655 AC: 19 AN: 290

European-Non Finnish (NFE) AF: 0.0441 AC: 2998 AN: 67996

Other (OTH) AF: 0.0421 AC: 89 AN: 2114

Alfa AF: 0.0318 Hom.: 27

Bravo AF: 0.0364

Asia WGS AF: 0.00809 AC: 28 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.0
DANN	Benign	0.63
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17195476; hg19: chr13-72771401;