rs17655948

Variant names:

• chr13-105415571-T-A
• rs17655948

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 0.302 in 151,996 control chromosomes in the GnomAD database, including 7,759 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 0.30 (7759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45806 AN: 151876 Hom.: 7754 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.302 AC: 45830 AN: 151996 Hom.: 7759 Cov.: 32 AF XY: 0.303 AC XY: 22543 AN XY: 74288

African (AFR) AF: 0.144 AC: 5992 AN: 41506

American (AMR) AF: 0.310 AC: 4729 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1527 AN: 3462

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5174

South Asian (SAS) AF: 0.364 AC: 1755 AN: 4818

European-Finnish (FIN) AF: 0.438 AC: 4621 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24990 AN: 67922

Other (OTH) AF: 0.341 AC: 720 AN: 2110

Alfa AF: 0.328 Hom.: 1039

Bravo AF: 0.288

Asia WGS AF: 0.281 AC: 979 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.059
DANN	Benign	0.47
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17655948; hg19: chr13-106067920;