11-14900334-G-A

Variant names:

• chr11-14900334-G-A
• rs10766197

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 0.36 in 152,040 control chromosomes in the GnomAD database, including 11,369 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 0.36 (11369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 91 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 = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54737 AN: 151922 Hom.: 11375 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.360 AC: 54736 AN: 152040 Hom.: 11369 Cov.: 32 AF XY: 0.361 AC XY: 26844 AN XY: 74310

African (AFR) AF: 0.148 AC: 6132 AN: 41478

American (AMR) AF: 0.345 AC: 5275 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1853 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4814

European-Finnish (FIN) AF: 0.410 AC: 4327 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31790 AN: 67962

Other (OTH) AF: 0.372 AC: 788 AN: 2116

Alfa AF: 0.425 Hom.: 36093

Bravo AF: 0.345

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.27
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs10766197; hg19: chr11-14921880;