14-82904686-G-T

Variant names:

• chr14-82904686-G-T
• rs7156012

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 0.482 in 151,786 control chromosomes in the GnomAD database, including 17,742 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 0.48 (17742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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: 0.481 AC: 73020 AN: 151668 Hom.: 17720 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.482 AC: 73093 AN: 151786 Hom.: 17742 Cov.: 32 AF XY: 0.481 AC XY: 35686 AN XY: 74138

African (AFR) AF: 0.485 AC: 20064 AN: 41406

American (AMR) AF: 0.444 AC: 6772 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1831 AN: 3462

East Asian (EAS) AF: 0.460 AC: 2357 AN: 5122

South Asian (SAS) AF: 0.451 AC: 2173 AN: 4814

European-Finnish (FIN) AF: 0.497 AC: 5218 AN: 10506

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32982 AN: 67922

Other (OTH) AF: 0.512 AC: 1082 AN: 2112

Alfa AF: 0.486 Hom.: 56442

Bravo AF: 0.476

Asia WGS AF: 0.439 AC: 1526 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs7156012; hg19: chr14-83371030;