rs4149013

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0136 AC: 563 AN: 41542

American (AMR) AF: 0.0381 AC: 582 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.135 AC: 696 AN: 5174

South Asian (SAS) AF: 0.0470 AC: 227 AN: 4826

European-Finnish (FIN) AF: 0.109 AC: 1159 AN: 10602

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0613 AC: 4166 AN: 67984

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0585 Hom.: 579

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4149013; hg19: chr12-21282410;