chr7-89998843-C-G

Variant names:

• chr7-89998843-C-G
• rs259160
• ENST00000478318.6:n.425-116288G>C

Variant summary

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

The ENST00000478318.6(STEAP2-AS1):​n.425-116288G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 151,468 control chromosomes in the GnomAD database, including 757 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 0.048 (757 hom., cov: 33)
• Consequence: STEAP2-AS1 ENST00000478318.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP2-AS1	NR_110029.2	n.425-116288G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP2-AS1	ENST00000478318.6	n.425-116288G>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7256 AN: 151350 Hom.: 750 Cov.: 33

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00681

Gnomad OTH AF: 0.0476

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

GnomAD4 genome AF: 0.0480 AC: 7275 AN: 151468 Hom.: 757 Cov.: 33 AF XY: 0.0527 AC XY: 3897 AN XY: 73996

African (AFR) AF: 0.0432 AC: 1788 AN: 41384

American (AMR) AF: 0.143 AC: 2167 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3460

East Asian (EAS) AF: 0.433 AC: 2230 AN: 5150

South Asian (SAS) AF: 0.0759 AC: 365 AN: 4808

European-Finnish (FIN) AF: 0.00988 AC: 104 AN: 10528

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.00680 AC: 460 AN: 67668

Other (OTH) AF: 0.0471 AC: 99 AN: 2100

Alfa AF: 0.00350 Hom.: 0

Bravo AF: 0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs259160; hg19: chr7-89628157;