rs10741613

Variant names:

• chr11-13172259-A-G
• rs10741613

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 0.605 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.744 AC: 30870 AN: 41492

American (AMR) AF: 0.543 AC: 8292 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1601 AN: 5188

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4818

European-Finnish (FIN) AF: 0.540 AC: 5707 AN: 10568

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39549 AN: 67984

Other (OTH) AF: 0.610 AC: 1285 AN: 2106

Alfa AF: 0.581 Hom.: 13235

Bravo AF: 0.612

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs10741613; hg19: chr11-13193806;