7-90095180-T-C

Variant summary

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

The NR_110029.2(STEAP2-AS1):n.424+114671A>G 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 0.0989 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 NR_110029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP2-AS1	NR_110029.2	n.424+114671A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP2-AS1	ENST00000478318.6	n.424+114671A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.0534

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.00810

Gnomad4 OTH AF: 0.0790

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.089
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2051958; hg19: chr7-89724494;