7-90008294-T-G

Position:

• chr7-90008294-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110029.2(STEAP2-AS1):​n.425-125739A>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 0.531 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 NR_110029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP2-AS1	NR_110029.2	n.425-125739A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP2-AS1	ENST00000478318.6	n.425-125739A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.564

Alfa AF: 0.513 Hom.: 2492

Bravo AF: 0.551

Asia WGS AF: 0.527 AC: 1830 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10245483; hg19: chr7-89637608;