rs12590429

Positions:

• chr14-23013731-G-A

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 0.0717 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0366

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.0918

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12590429; hg19: chr14-23482940;