14-98379194-C-T

Variant names:

• chr14-98379194-C-T
• rs873196

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 0.679 in 152,066 control chromosomes in the GnomAD database, including 35,633 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 0.68 (35633 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 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: 0.679 AC: 103141 AN: 151948 Hom.: 35601 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.679 AC: 103222 AN: 152066 Hom.: 35633 Cov.: 32 AF XY: 0.686 AC XY: 51022 AN XY: 74330

African (AFR) AF: 0.776 AC: 32182 AN: 41468

American (AMR) AF: 0.710 AC: 10865 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2330 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4423 AN: 5170

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4822

European-Finnish (FIN) AF: 0.677 AC: 7151 AN: 10570

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40338 AN: 67964

Other (OTH) AF: 0.689 AC: 1452 AN: 2106

Alfa AF: 0.652 Hom.: 27051

Bravo AF: 0.686

Asia WGS AF: 0.797 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.18
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs873196; hg19: chr14-98845531;