chr11-20139419-G-A

Variant names:

• chr11-20139419-G-A
• rs961746

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 0.418 in 151,832 control chromosomes in the GnomAD database, including 13,533 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 0.42 (13533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.418 AC: 63441 AN: 151714 Hom.: 13513 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.418 AC: 63496 AN: 151832 Hom.: 13533 Cov.: 33 AF XY: 0.423 AC XY: 31401 AN XY: 74172

African (AFR) AF: 0.491 AC: 20324 AN: 41392

American (AMR) AF: 0.475 AC: 7236 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5160

South Asian (SAS) AF: 0.478 AC: 2301 AN: 4816

European-Finnish (FIN) AF: 0.435 AC: 4564 AN: 10502

Middle Eastern (MID) AF: 0.259 AC: 75 AN: 290

European-Non Finnish (NFE) AF: 0.367 AC: 24913 AN: 67944

Other (OTH) AF: 0.386 AC: 813 AN: 2106

Alfa AF: 0.373 Hom.: 12979

Bravo AF: 0.421

Asia WGS AF: 0.413 AC: 1436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.45
DANN	Benign	0.67
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs961746; hg19: chr11-20160965;