rs259160

chr7-89998843-C-Gchr7-89998843-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110029.2(STEAP2-AS1):n.425-116288G>C variant causes a intron, non coding transcript 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 NR_110029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
STEAP2-AS1	NR_110029.2	n.425-116288G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP2-AS1	ENST00000478318.6	n.425-116288G>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.0759

Gnomad4 FIN AF: 0.00988

Gnomad4 NFE AF: 0.00680

Gnomad4 OTH AF: 0.0471

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259160; hg19: chr7-89628157;