rs1952299

Variant names:

• chr14-97256934-C-A
• rs1952299

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 0.165 in 151,844 control chromosomes in the GnomAD database, including 3,424 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 0.17 (3424 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.165 AC: 25015 AN: 151726 Hom.: 3404 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.165 AC: 25074 AN: 151844 Hom.: 3424 Cov.: 31 AF XY: 0.161 AC XY: 11952 AN XY: 74254

African (AFR) AF: 0.374 AC: 15445 AN: 41324

American (AMR) AF: 0.104 AC: 1582 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1076 AN: 5134

South Asian (SAS) AF: 0.105 AC: 506 AN: 4812

European-Finnish (FIN) AF: 0.0406 AC: 429 AN: 10574

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0810 AC: 5505 AN: 67952

Other (OTH) AF: 0.138 AC: 291 AN: 2110

Alfa AF: 0.124 Hom.: 298

Bravo AF: 0.180

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.32
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1952299; hg19: chr14-97723271;