14-91950020-A-G

Variant names:

• chr14-91950020-A-G
• rs2498852

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 0.539 in 152,078 control chromosomes in the GnomAD database, including 22,977 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 0.54 (22977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81872 AN: 151960 Hom.: 22944 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.539 AC: 81959 AN: 152078 Hom.: 22977 Cov.: 32 AF XY: 0.534 AC XY: 39702 AN XY: 74328

African (AFR) AF: 0.694 AC: 28756 AN: 41456

American (AMR) AF: 0.448 AC: 6839 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2081 AN: 5174

South Asian (SAS) AF: 0.613 AC: 2954 AN: 4820

European-Finnish (FIN) AF: 0.452 AC: 4788 AN: 10584

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32843 AN: 67976

Other (OTH) AF: 0.536 AC: 1133 AN: 2114

Alfa AF: 0.514 Hom.: 11101

Bravo AF: 0.540

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2498852; hg19: chr14-92416364;