rs11622505

Variant names:

• chr14-92851221-A-G
• rs11622505

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 0.135 in 152,114 control chromosomes in the GnomAD database, including 1,765 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 0.13 (1765 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.135 AC: 20464 AN: 151996 Hom.: 1765 Cov.: 31

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20462 AN: 152114 Hom.: 1765 Cov.: 31 AF XY: 0.128 AC XY: 9526 AN XY: 74360

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0994

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.152

Alfa AF: 0.163 Hom.: 659

Bravo AF: 0.132

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11622505; hg19: chr14-93317566;