14-94691009-A-C

Variant names:

• chr14-94691009-A-C
• rs9323914

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 0.244 in 152,014 control chromosomes in the GnomAD database, including 4,842 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 0.24 (4842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37065 AN: 151896 Hom.: 4821 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.244 AC: 37140 AN: 152014 Hom.: 4842 Cov.: 32 AF XY: 0.244 AC XY: 18096 AN XY: 74300

African (AFR) AF: 0.294 AC: 12206 AN: 41470

American (AMR) AF: 0.183 AC: 2800 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2533 AN: 5144

South Asian (SAS) AF: 0.301 AC: 1445 AN: 4804

European-Finnish (FIN) AF: 0.177 AC: 1877 AN: 10582

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14950 AN: 67966

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.215 Hom.: 4136

Bravo AF: 0.246

Asia WGS AF: 0.418 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.33
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs9323914; hg19: chr14-95157346;