chr14-97256934-C-A

Variant names:

• chr14-97256934-C-A
• rs1952299

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 0.165 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.165 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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.138

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1952299; hg19: chr14-97723271;