chr14-83714525-G-A

Variant names:

• chr14-83714525-G-A
• rs10873350

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.771 in 152,068 control chromosomes in the GnomAD database, including 45,748 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 0.77 (45748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.771 AC: 117185 AN: 151950 Hom.: 45696 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.771 AC: 117297 AN: 152068 Hom.: 45748 Cov.: 32 AF XY: 0.779 AC XY: 57880 AN XY: 74316

African (AFR) AF: 0.851 AC: 35299 AN: 41502

American (AMR) AF: 0.795 AC: 12119 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2649 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4950 AN: 5138

South Asian (SAS) AF: 0.845 AC: 4080 AN: 4826

European-Finnish (FIN) AF: 0.802 AC: 8498 AN: 10598

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47223 AN: 67964

Other (OTH) AF: 0.742 AC: 1568 AN: 2114

Alfa AF: 0.751 Hom.: 8464

Bravo AF: 0.776

Asia WGS AF: 0.886 AC: 3077 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	9.1
DANN	Benign	0.54
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10873350; hg19: chr14-84180869;