rs10741613

Variant names:

• chr11-13172259-A-G
• rs10741613

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 0.605 in 152,114 control chromosomes in the GnomAD database, including 28,726 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 0.60 (28726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.605 AC: 91966 AN: 151996 Hom.: 28713 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.605 AC: 92016 AN: 152114 Hom.: 28726 Cov.: 32 AF XY: 0.597 AC XY: 44383 AN XY: 74374

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.610

Alfa AF: 0.579 Hom.: 11715

Bravo AF: 0.612

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10741613; hg19: chr11-13193806;