11-15811201-G-T

Variant names:

• chr11-15811201-G-T
• rs1920676

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 0.406 in 151,888 control chromosomes in the GnomAD database, including 14,511 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 0.41 (14511 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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: 0.406 AC: 61612 AN: 151770 Hom.: 14468 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.406 AC: 61713 AN: 151888 Hom.: 14511 Cov.: 33 AF XY: 0.405 AC XY: 30079 AN XY: 74254

African (AFR) AF: 0.634 AC: 26270 AN: 41430

American (AMR) AF: 0.489 AC: 7461 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3466

East Asian (EAS) AF: 0.237 AC: 1218 AN: 5134

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4810

European-Finnish (FIN) AF: 0.250 AC: 2650 AN: 10594

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20000 AN: 67890

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.195 Hom.: 382

Bravo AF: 0.434

Asia WGS AF: 0.388 AC: 1347 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1920676; hg19: chr11-15832747;