rs11622652

Variant names:

• chr14-93865470-G-A
• rs11622652

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.533

Alfa AF: 0.560 Hom.: 33746

Bravo AF: 0.507

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11622652; hg19: chr14-94331816;