12-21130019-T-G

Variant names:

• chr12-21130019-T-G
• rs4149014
• ENST00000593147.5:n.*115-1104T>G

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*115-1104T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,102 control chromosomes in the GnomAD database, including 402 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 0.038 (402 hom., cov: 32)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

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 = 0.304 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.*115-1104T>G		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5762 AN: 151984 Hom.: 401 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00250

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0379 AC: 5771 AN: 152102 Hom.: 402 Cov.: 32 AF XY: 0.0435 AC XY: 3232 AN XY: 74342

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0863

Gnomad4 NFE AF: 0.00250

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.00991 Hom.: 268

Bravo AF: 0.0353

Asia WGS AF: 0.163 AC: 564 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	7.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4149014; hg19: chr12-21282953;