14-93129246-A-C

Variant names:

• chr14-93129246-A-C
• rs11624776

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 0.259 in 152,190 control chromosomes in the GnomAD database, including 5,896 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 0.26 (5896 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.337 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: 0.259 AC: 39434 AN: 152072 Hom.: 5890 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.259 AC: 39449 AN: 152190 Hom.: 5896 Cov.: 33 AF XY: 0.262 AC XY: 19503 AN XY: 74406

African (AFR) AF: 0.104 AC: 4338 AN: 41550

American (AMR) AF: 0.345 AC: 5264 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3466

East Asian (EAS) AF: 0.157 AC: 814 AN: 5186

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3299 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22067 AN: 67992

Other (OTH) AF: 0.293 AC: 620 AN: 2114

Alfa AF: 0.283 Hom.: 11215

Bravo AF: 0.252

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11624776; hg19: chr14-93595591;