chr7-90090173-C-T

Variant names:

• chr7-90090173-C-T
• rs11978340
• ENST00000478318.6:n.424+119678G>A

Variant summary

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

The ENST00000478318.6(STEAP2-AS1):​n.424+119678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,708 control chromosomes in the GnomAD database, including 7,495 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 0.29 (7495 hom., cov: 32)
• Consequence: STEAP2-AS1 ENST00000478318.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2-AS1	NR_110029.2		n.424+119678G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2-AS1	ENST00000478318.6	TSL:3	n.424+119678G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43861 AN: 151590 Hom.: 7472 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.289 AC: 43919 AN: 151708 Hom.: 7495 Cov.: 32 AF XY: 0.296 AC XY: 21961 AN XY: 74104

African (AFR) AF: 0.378 AC: 15639 AN: 41348

American (AMR) AF: 0.379 AC: 5772 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3793 AN: 5174

South Asian (SAS) AF: 0.338 AC: 1626 AN: 4808

European-Finnish (FIN) AF: 0.222 AC: 2318 AN: 10464

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13545 AN: 67910

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.222 Hom.: 4084

Bravo AF: 0.306

Asia WGS AF: 0.501 AC: 1739 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.36
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11978340; hg19: chr7-89719487;