rs1514928

Variant names:

• chr14-62211585-C-A
• rs1514928

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 0.112 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.112 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

African (AFR) AF: 0.180 AC: 7483 AN: 41490

American (AMR) AF: 0.0851 AC: 1301 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5180

South Asian (SAS) AF: 0.188 AC: 905 AN: 4820

European-Finnish (FIN) AF: 0.0793 AC: 839 AN: 10582

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0843 AC: 5736 AN: 68004

Other (OTH) AF: 0.107 AC: 225 AN: 2110

Alfa AF: 0.0941 Hom.: 2544

Bravo AF: 0.112

Asia WGS AF: 0.115 AC: 399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1514928; hg19: chr14-62678303;