rs11622895

chr14-20846841-C-T

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 0.493 in 151,944 control chromosomes in the GnomAD database, including 19,556 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 0.49 (19556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74845 AN: 151826 Hom.: 19550 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.493 AC: 74868 AN: 151944 Hom.: 19556 Cov.: 31 AF XY: 0.496 AC XY: 36880 AN XY: 74280

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.472

Alfa AF: 0.551 Hom.: 34708

Bravo AF: 0.486

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11622895; hg19: chr14-21315000;