rs12589195

Variant names:

• chr14-93147717-C-A
• rs12589195

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 0.194 in 151,846 control chromosomes in the GnomAD database, including 3,459 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 0.19 (3459 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.194 AC: 29412 AN: 151730 Hom.: 3454 Cov.: 30

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.194 AC: 29424 AN: 151846 Hom.: 3459 Cov.: 30 AF XY: 0.196 AC XY: 14572 AN XY: 74180

African (AFR) AF: 0.0796 AC: 3300 AN: 41434

American (AMR) AF: 0.188 AC: 2865 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2312 AN: 5152

South Asian (SAS) AF: 0.254 AC: 1220 AN: 4804

European-Finnish (FIN) AF: 0.249 AC: 2623 AN: 10532

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15752 AN: 67928

Other (OTH) AF: 0.185 AC: 390 AN: 2104

Alfa AF: 0.215 Hom.: 9853

Bravo AF: 0.184

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.51
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12589195; hg19: chr14-93614062;