chr14-96201939-G-A

Variant names:

• chr14-96201939-G-A
• rs12431885

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 0.0663 in 152,000 control chromosomes in the GnomAD database, including 880 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 0.066 (880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.242 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: 0.0663 AC: 10066 AN: 151882 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0663 AC: 10082 AN: 152000 Hom.: 880 Cov.: 32 AF XY: 0.0725 AC XY: 5384 AN XY: 74278

African (AFR) AF: 0.0284 AC: 1179 AN: 41470

American (AMR) AF: 0.249 AC: 3801 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1267 AN: 5132

South Asian (SAS) AF: 0.0692 AC: 332 AN: 4798

European-Finnish (FIN) AF: 0.0695 AC: 734 AN: 10566

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2489 AN: 67974

Other (OTH) AF: 0.0693 AC: 146 AN: 2106

Alfa AF: 0.0191 Hom.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.51
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12431885; hg19: chr14-96668276;