rs12590429

Variant names:

• chr14-23013731-G-A
• rs12590429

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 0.0717 in 152,190 control chromosomes in the GnomAD database, including 489 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 0.072 (489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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: 0.0717 AC: 10896 AN: 152072 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.0365

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0617

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0717 AC: 10913 AN: 152190 Hom.: 489 Cov.: 32 AF XY: 0.0749 AC XY: 5572 AN XY: 74402

African (AFR) AF: 0.0366 AC: 1519 AN: 41546

American (AMR) AF: 0.0616 AC: 941 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3470

East Asian (EAS) AF: 0.0541 AC: 280 AN: 5174

South Asian (SAS) AF: 0.140 AC: 678 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5490 AN: 68010

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.0752 Hom.: 111

Bravo AF: 0.0625

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12590429; hg19: chr14-23482940;