chr7-90008294-T-G

Variant names:

• chr7-90008294-T-G
• rs10245483
• ENST00000478318.6:n.425-125739A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000478318.6(STEAP2-AS1):​n.425-125739A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,938 control chromosomes in the GnomAD database, including 21,686 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 0.53 (21686 hom., cov: 32)
• Consequence: STEAP2-AS1 ENST00000478318.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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.425-125739A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2-AS1	ENST00000478318.6	TSL:3	n.425-125739A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80652 AN: 151820 Hom.: 21662 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.531 AC: 80727 AN: 151938 Hom.: 21686 Cov.: 32 AF XY: 0.528 AC XY: 39199 AN XY: 74236

African (AFR) AF: 0.532 AC: 22045 AN: 41440

American (AMR) AF: 0.608 AC: 9264 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2150 AN: 3462

East Asian (EAS) AF: 0.613 AC: 3166 AN: 5164

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4812

European-Finnish (FIN) AF: 0.425 AC: 4478 AN: 10544

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35515 AN: 67952

Other (OTH) AF: 0.564 AC: 1189 AN: 2110

Alfa AF: 0.513 Hom.: 2604

Bravo AF: 0.551

Asia WGS AF: 0.527 AC: 1830 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs10245483; hg19: chr7-89637608;