14-20360873-C-T

Variant names:

• chr14-20360873-C-T
• rs4981998

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 0.21 in 151,984 control chromosomes in the GnomAD database, including 3,855 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 0.21 (3855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 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: 0.210 AC: 31940 AN: 151866 Hom.: 3858 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.210 AC: 31942 AN: 151984 Hom.: 3855 Cov.: 32 AF XY: 0.212 AC XY: 15703 AN XY: 74242

African (AFR) AF: 0.0974 AC: 4037 AN: 41454

American (AMR) AF: 0.201 AC: 3070 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1447 AN: 5188

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4816

European-Finnish (FIN) AF: 0.289 AC: 3036 AN: 10494

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

European-Non Finnish (NFE) AF: 0.254 AC: 17295 AN: 67988

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.140 Hom.: 318

Bravo AF: 0.196

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4981998; hg19: chr14-20829032;