ENST00000593147.5:n.*115-1104T>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593147.5(ENSG00000257062):​n.*115-1104T>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
• Publications: 11 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 = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593147.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257062	ENST00000593147.5	TSL:5	n.*115-1104T>G		intron	N/A	ENSP00000467209.1
	ENSG00000257062	ENST00000543498.5	TSL:4	n.279-11495T>G		intron	N/A	ENSP00000454306.1
	ENSG00000257062	ENST00000585342.5	TSL:4	n.*101-1104T>G		intron	N/A	ENSP00000467594.1

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

African (AFR) AF: 0.0541 AC: 2245 AN: 41512

American (AMR) AF: 0.0339 AC: 517 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1635 AN: 5158

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4816

European-Finnish (FIN) AF: 0.0863 AC: 914 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00250 AC: 170 AN: 67990

Other (OTH) AF: 0.0374 AC: 79 AN: 2112

Alfa AF: 0.0136 Hom.: 667

Bravo AF: 0.0353

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.76
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4149014; hg19: chr12-21282953;