14-96201939-G-C

Variant names:

• chr14-96201939-G-C
• 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 0.133 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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

African (AFR) AF: 0.141 AC: 5859 AN: 41456

American (AMR) AF: 0.166 AC: 2531 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1493 AN: 5132

South Asian (SAS) AF: 0.180 AC: 861 AN: 4796

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7470 AN: 67960

Other (OTH) AF: 0.141 AC: 296 AN: 2104

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
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;