11-13206459-G-T

Position:

• chr11-13206459-G-T

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 0.724 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.754

Alfa AF: 0.779 Hom.: 17571

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7941871; hg19: chr11-13228006;