ENST00000452153.4:n.330+360A>G

Variant names:

• chr17-19631121-A-G
• rs9903027
• ENST00000452153.4:n.330+360A>G

Variant summary

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

The ENST00000452153.4(ENSG00000290544):​n.330+360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 150,784 control chromosomes in the GnomAD database, including 18,228 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 0.47 (18228 hom., cov: 30)
• Consequence: ENSG00000290544 ENST00000452153.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 6 publications found

Genes affected

ENSG00000290544 (HGNC:):

SLC47A1P2 (HGNC:53866): (SLC47A1 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452153.4. 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
	SLC47A1P2	NR_170227.1		n.751+360A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290544	ENST00000452153.4	TSL:2	n.330+360A>G		intron	N/A
	SLC47A1P2	ENST00000574288.2	TSL:6	n.419+369A>G		intron	N/A
	ENSG00000262769	ENST00000841120.1		n.218+15816T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 70860 AN: 150668 Hom.: 18217 Cov.: 30

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.0907

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.470 AC: 70891 AN: 150784 Hom.: 18228 Cov.: 30 AF XY: 0.463 AC XY: 34154 AN XY: 73706

African (AFR) AF: 0.588 AC: 23887 AN: 40608

American (AMR) AF: 0.345 AC: 5231 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1828 AN: 3458

East Asian (EAS) AF: 0.0909 AC: 470 AN: 5168

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4798

European-Finnish (FIN) AF: 0.512 AC: 5381 AN: 10500

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31045 AN: 67798

Other (OTH) AF: 0.464 AC: 972 AN: 2094

Alfa AF: 0.444 Hom.: 7222

Bravo AF: 0.466

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9903027; hg19: chr17-19534434;