rs10741613

Positions:

• chr11-13172259-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;