14-96201939-G-C

Variant names:

• chr14-96201939-G-C
• rs12431885

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 0.133 in 151,972 control chromosomes in the GnomAD database, including 1,509 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 0.13 (1509 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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: 0.133 AC: 20186 AN: 151854 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.133 AC: 20197 AN: 151972 Hom.: 1509 Cov.: 32 AF XY: 0.136 AC XY: 10104 AN XY: 74264

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0371 Hom.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.39

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;