14-94327349-G-T

Variant names:

• chr14-94327349-G-T
• rs12589136

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 0.2 in 152,074 control chromosomes in the GnomAD database, including 3,441 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 0.20 (3441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 19 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 = 0.373 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: 0.200 AC: 30436 AN: 151954 Hom.: 3433 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.200 AC: 30461 AN: 152074 Hom.: 3441 Cov.: 32 AF XY: 0.203 AC XY: 15094 AN XY: 74340

African (AFR) AF: 0.150 AC: 6202 AN: 41472

American (AMR) AF: 0.147 AC: 2248 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.387 AC: 2000 AN: 5166

South Asian (SAS) AF: 0.366 AC: 1766 AN: 4830

European-Finnish (FIN) AF: 0.213 AC: 2250 AN: 10560

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14481 AN: 67986

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.206 Hom.: 10176

Bravo AF: 0.188

Asia WGS AF: 0.342 AC: 1186 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12589136; hg19: chr14-94793686;