chr11-13169746-G-T

Variant names:

• chr11-13169746-G-T
• rs1481871

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 0.617 in 152,066 control chromosomes in the GnomAD database, including 29,944 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 0.62 (29944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 5 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 = 0.765 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93766 AN: 151948 Hom.: 29929 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.617 AC: 93821 AN: 152066 Hom.: 29944 Cov.: 32 AF XY: 0.609 AC XY: 45251 AN XY: 74324

African (AFR) AF: 0.772 AC: 32015 AN: 41486

American (AMR) AF: 0.547 AC: 8359 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1598 AN: 5178

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5744 AN: 10560

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39895 AN: 67968

Other (OTH) AF: 0.623 AC: 1318 AN: 2114

Alfa AF: 0.592 Hom.: 112727

Bravo AF: 0.625

Asia WGS AF: 0.412 AC: 1433 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	0.79
DANN	Benign	0.39
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1481871; hg19: chr11-13191293;