rs4149015

Variant names:

• chr12-21130388-G-A
• rs4149015
• ENST00000593147.5:n.*115-735G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-21130388-G-A
• chr12-21130388-G-C
• chr12-21130388-G-T

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*115-735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 151,902 control chromosomes in the GnomAD database, including 282 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 0.051 (282 hom., cov: 32)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 73 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257062	ENST00000593147.5	TSL:5	n.*115-735G>A		intron	N/A	ENSP00000467209.1	K7EP34
	ENSG00000257062	ENST00000543498.5	TSL:4	n.279-11126G>A		intron	N/A	ENSP00000454306.1	H3BMA8
	ENSG00000257062	ENST00000585342.5	TSL:4	n.*101-735G>A		intron	N/A	ENSP00000467594.1	K7EPY8

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7766 AN: 151784 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0508

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0511 AC: 7767 AN: 151902 Hom.: 282 Cov.: 32 AF XY: 0.0528 AC XY: 3922 AN XY: 74226

African (AFR) AF: 0.0136 AC: 564 AN: 41432

American (AMR) AF: 0.0368 AC: 561 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5156

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1160 AN: 10548

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0609 AC: 4136 AN: 67924

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0473 Hom.: 120

Bravo AF: 0.0437

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.088
DANN	Benign	0.13
PhyloP100		-3.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4149015;

hg19: chr12-21283322;