rs1514928

Variant names:

• chr14-62211585-C-A
• rs1514928

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 0.112 in 152,148 control chromosomes in the GnomAD database, including 1,155 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 0.11 (1155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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: 0.112 AC: 17093 AN: 152030 Hom.: 1154 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.112 AC: 17107 AN: 152148 Hom.: 1155 Cov.: 32 AF XY: 0.113 AC XY: 8382 AN XY: 74376

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0851

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0907 Hom.: 1064

Bravo AF: 0.112

Asia WGS AF: 0.115 AC: 399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1514928; hg19: chr14-62678303;