rs11159647

Variant names:

• chr14-84308865-G-A
• rs11159647

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 0.337 in 151,940 control chromosomes in the GnomAD database, including 10,690 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 0.34 (10690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) 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: 0.337 AC: 51208 AN: 151822 Hom.: 10690 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.337 AC: 51194 AN: 151940 Hom.: 10690 Cov.: 32 AF XY: 0.337 AC XY: 24999 AN XY: 74240

African (AFR) AF: 0.0913 AC: 3782 AN: 41438

American (AMR) AF: 0.386 AC: 5885 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1274 AN: 5160

South Asian (SAS) AF: 0.501 AC: 2412 AN: 4810

European-Finnish (FIN) AF: 0.364 AC: 3830 AN: 10528

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30994 AN: 67976

Other (OTH) AF: 0.376 AC: 794 AN: 2110

Alfa AF: 0.387 Hom.: 15441

Bravo AF: 0.329

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.18
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs11159647; hg19: chr14-84775209;