rs11622652

Variant names:

• chr14-93865470-G-A
• rs11622652

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 0.511 in 152,014 control chromosomes in the GnomAD database, including 20,357 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 0.51 (20357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 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: 0.511 AC: 77665 AN: 151896 Hom.: 20359 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.511 AC: 77701 AN: 152014 Hom.: 20357 Cov.: 32 AF XY: 0.506 AC XY: 37559 AN XY: 74282

African (AFR) AF: 0.457 AC: 18920 AN: 41444

American (AMR) AF: 0.484 AC: 7386 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5166

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5446 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 39002 AN: 67966

Other (OTH) AF: 0.533 AC: 1127 AN: 2114

Alfa AF: 0.554 Hom.: 84754

Bravo AF: 0.507

Asia WGS AF: 0.349 AC: 1216 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	0.030
DANN	Benign	0.60
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11622652; hg19: chr14-94331816;