11-13206459-G-T

Variant names:

• chr11-13206459-G-T
• rs7941871

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 0.724 in 152,036 control chromosomes in the GnomAD database, including 40,996 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 0.72 (40996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 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: 0.724 AC: 110031 AN: 151918 Hom.: 40983 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.724 AC: 110084 AN: 152036 Hom.: 40996 Cov.: 32 AF XY: 0.718 AC XY: 53335 AN XY: 74298

African (AFR) AF: 0.576 AC: 23877 AN: 41454

American (AMR) AF: 0.812 AC: 12410 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2867 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2088 AN: 5146

South Asian (SAS) AF: 0.682 AC: 3281 AN: 4812

European-Finnish (FIN) AF: 0.703 AC: 7418 AN: 10548

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55528 AN: 68004

Other (OTH) AF: 0.754 AC: 1593 AN: 2114

Alfa AF: 0.780 Hom.: 20259

Bravo AF: 0.726

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs7941871; hg19: chr11-13228006;