7-90095180-T-C

Variant names:

• chr7-90095180-T-C
• rs2051958
• ENST00000478318.6:n.424+114671A>G

Variant summary

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

The ENST00000478318.6(STEAP2-AS1):​n.424+114671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,130 control chromosomes in the GnomAD database, including 1,785 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 0.099 (1785 hom., cov: 32)
• Consequence: STEAP2-AS1 ENST00000478318.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000478318.6. 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
	STEAP2-AS1	NR_110029.2		n.424+114671A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2-AS1	ENST00000478318.6	TSL:3	n.424+114671A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 15003 AN: 152012 Hom.: 1777 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.0535

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00812

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0989 AC: 15042 AN: 152130 Hom.: 1785 Cov.: 32 AF XY: 0.0998 AC XY: 7425 AN XY: 74378

African (AFR) AF: 0.247 AC: 10231 AN: 41460

American (AMR) AF: 0.117 AC: 1792 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5162

South Asian (SAS) AF: 0.0534 AC: 257 AN: 4816

European-Finnish (FIN) AF: 0.00320 AC: 34 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00810 AC: 551 AN: 68004

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0551 Hom.: 112

Bravo AF: 0.116

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.089
DANN	Benign	0.32
PhyloP100		-2.4

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: rs2051958;

hg19: chr7-89724494;