ENST00000478318.6:n.425-112108G>A

Variant names:

• chr7-89994663-C-T
• rs10487093
• ENST00000478318.6:n.425-112108G>A

Variant summary

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

The ENST00000478318.6(STEAP2-AS1):​n.425-112108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0571 in 152,174 control chromosomes in the GnomAD database, including 541 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 0.057 (541 hom., cov: 32)
• Consequence: STEAP2-AS1 ENST00000478318.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 0 publications found

Genes affected

STEAP2-AS1 (HGNC:40820): (STEAP2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP2-AS1	NR_110029.2	n.425-112108G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP2-AS1	ENST00000478318.6	n.425-112108G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8662 AN: 152056 Hom.: 535 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.00481

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0571 AC: 8685 AN: 152174 Hom.: 541 Cov.: 32 AF XY: 0.0557 AC XY: 4147 AN XY: 74388

African (AFR) AF: 0.154 AC: 6390 AN: 41480

American (AMR) AF: 0.0349 AC: 534 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0584 AC: 282 AN: 4826

European-Finnish (FIN) AF: 0.00481 AC: 51 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0175 AC: 1190 AN: 68026

Other (OTH) AF: 0.0537 AC: 113 AN: 2106

Alfa AF: 0.0170 Hom.: 22

Bravo AF: 0.0637

Asia WGS AF: 0.0300 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.33
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10487093; hg19: chr7-89623977;