rs17195476

chr13-72197263-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 128 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0195

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0358 Hom.: 18

Bravo AF: 0.0364

Asia WGS AF: 0.00809 AC: 28 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.0
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17195476; hg19: chr13-72771401;