14-20360960-C-T

Variant names:

• chr14-20360960-C-T
• rs2678681

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 0.124 in 134,664 control chromosomes in the GnomAD database, including 1,087 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 0.12 (1087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 16743 AN: 134580 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.124 AC: 16749 AN: 134664 Hom.: 1087 Cov.: 32 AF XY: 0.125 AC XY: 8195 AN XY: 65702

African (AFR) AF: 0.193 AC: 6452 AN: 33384

American (AMR) AF: 0.155 AC: 2189 AN: 14136

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 333 AN: 3280

East Asian (EAS) AF: 0.186 AC: 874 AN: 4708

South Asian (SAS) AF: 0.168 AC: 680 AN: 4040

European-Finnish (FIN) AF: 0.0756 AC: 722 AN: 9556

Middle Eastern (MID) AF: 0.186 AC: 52 AN: 280

European-Non Finnish (NFE) AF: 0.0819 AC: 5124 AN: 62550

Other (OTH) AF: 0.126 AC: 235 AN: 1860

Alfa AF: 0.0861 Hom.: 971

Bravo AF: 0.121

Asia WGS AF: 0.181 AC: 624 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.5
DANN	Benign	0.28
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2678681; hg19: chr14-20829119;