14-20499485-T-C

Variant names:

• chr14-20499485-T-C
• rs4982140

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 0.651 in 152,162 control chromosomes in the GnomAD database, including 34,727 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 0.65 (34727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 5 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 = 0.884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98984 AN: 152042 Hom.: 34713 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.651 AC: 99031 AN: 152162 Hom.: 34727 Cov.: 33 AF XY: 0.653 AC XY: 48591 AN XY: 74390

African (AFR) AF: 0.365 AC: 15142 AN: 41480

American (AMR) AF: 0.748 AC: 11438 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3472

East Asian (EAS) AF: 0.906 AC: 4699 AN: 5186

South Asian (SAS) AF: 0.709 AC: 3419 AN: 4824

European-Finnish (FIN) AF: 0.712 AC: 7536 AN: 10590

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52029 AN: 67992

Other (OTH) AF: 0.689 AC: 1458 AN: 2116

Alfa AF: 0.732 Hom.: 87074

Bravo AF: 0.646

Asia WGS AF: 0.791 AC: 2754 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	3.9
DANN	Benign	0.48
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4982140; hg19: chr14-20967644;