rs12432394

Variant names:

• chr14-21560810-C-T
• rs12432394

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 0.198 in 151,044 control chromosomes in the GnomAD database, including 3,594 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 0.20 (3594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 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: 0.198 AC: 29879 AN: 150930 Hom.: 3588 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.198 AC: 29906 AN: 151044 Hom.: 3594 Cov.: 32 AF XY: 0.196 AC XY: 14488 AN XY: 73794

African (AFR) AF: 0.172 AC: 6986 AN: 40614

American (AMR) AF: 0.313 AC: 4757 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 754 AN: 3466

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5176

South Asian (SAS) AF: 0.147 AC: 709 AN: 4808

European-Finnish (FIN) AF: 0.152 AC: 1597 AN: 10522

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14427 AN: 67944

Other (OTH) AF: 0.180 AC: 377 AN: 2096

Alfa AF: 0.212 Hom.: 481

Bravo AF: 0.207

Asia WGS AF: 0.0980 AC: 343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.40
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs12432394; hg19: chr14-22028941;