rs838079

Positions:

• chr2-119250136-G-A

Variant summary

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

The NM_182915.3(STEAP3):​c.1050+1930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,210 control chromosomes in the GnomAD database, including 2,410 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 0.14 (2410 hom., cov: 33)
• Consequence: STEAP3 NM_182915.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

STEAP3 (HGNC:24592): (STEAP3 metalloreductase) This gene encodes a multipass membrane protein that functions as an iron transporter. The encoded protein can reduce both iron (Fe3+) and copper (Cu2+) cations. This protein may mediate downstream responses to p53, including promoting apoptosis. Deficiency in this gene can cause anemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

STEAP3-AS1 (HGNC:41053): (STEAP3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP3	NM_182915.3	c.1050+1930G>A		intron_variant		ENST00000393110.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP3	ENST00000393110.7	c.1050+1930G>A		intron_variant		1	NM_182915.3
STEAP3-AS1	ENST00000654197.1	n.112-1774C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21021 AN: 152092 Hom.: 2406 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0710

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.138 AC: 21048 AN: 152210 Hom.: 2410 Cov.: 33 AF XY: 0.133 AC XY: 9898 AN XY: 74440

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0710

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0827

Gnomad4 OTH AF: 0.105

Alfa AF: 0.141 Hom.: 335

Bravo AF: 0.149

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs838079; hg19: chr2-120007712;