rs12431885

Variant names:

• chr14-96201939-G-A
• rs12431885

Your query was ambiguous. Multiple possible variants found:

• chr14-96201939-G-A
• chr14-96201939-G-C
• chr14-96201939-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.0191 Hom.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12431885; hg19: chr14-96668276;