14-82484084-T-C

Variant names:

• chr14-82484084-T-C
• rs10483956

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 0.195 in 152,002 control chromosomes in the GnomAD database, including 3,327 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 0.19 (3327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29558 AN: 151882 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29571 AN: 152002 Hom.: 3327 Cov.: 32 AF XY: 0.199 AC XY: 14808 AN XY: 74296

African (AFR) AF: 0.163 AC: 6783 AN: 41506

American (AMR) AF: 0.204 AC: 3111 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 588 AN: 3468

East Asian (EAS) AF: 0.541 AC: 2785 AN: 5146

South Asian (SAS) AF: 0.352 AC: 1694 AN: 4810

European-Finnish (FIN) AF: 0.153 AC: 1620 AN: 10584

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12360 AN: 67948

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.188 Hom.: 1928

Bravo AF: 0.194

Asia WGS AF: 0.453 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.84
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10483956; hg19: chr14-82950428;