14-20360873-C-T

Variant names:

• chr14-20360873-C-T
• rs4981998

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.210 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

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.208

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981998; hg19: chr14-20829032;