rs4149013

Variant names:

• chr12-21129476-A-G
• rs4149013
• ENST00000593147.5:n.*115-1647A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593147.5(ENSG00000257062):​n.*115-1647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0518 in 152,190 control chromosomes in the GnomAD database, including 290 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 0.052 (290 hom., cov: 32)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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
ENSG00000257062	ENST00000593147.5	n.*115-1647A>G		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7877 AN: 152072 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0518 AC: 7878 AN: 152190 Hom.: 290 Cov.: 32 AF XY: 0.0536 AC XY: 3990 AN XY: 74418

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0381

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0470

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0599 Hom.: 454

Bravo AF: 0.0446

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4149013; hg19: chr12-21282410;