rs17655948

Positions:

• chr13-105415571-T-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.341

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17655948; hg19: chr13-106067920;