rs1867749

Variant names:

• chr2-119256336-C-G
• rs1867749
• NM_182915.3:c.1215+1488C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-119256336-C-G
• chr2-119256336-C-T

Variant summary

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

The NM_182915.3(STEAP3):​c.1215+1488C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,998 control chromosomes in the GnomAD database, including 10,574 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 0.36 (10574 hom., cov: 32)
• Consequence: STEAP3 NM_182915.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP3	NM_182915.3	c.1215+1488C>G		intron_variant	Intron 5 of 5	ENST00000393110.7	NP_878919.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP3	ENST00000393110.7	c.1215+1488C>G		intron_variant	Intron 5 of 5	1	NM_182915.3	ENSP00000376822.2

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54971 AN: 151882 Hom.: 10567 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.362 AC: 54996 AN: 151998 Hom.: 10574 Cov.: 32 AF XY: 0.360 AC XY: 26733 AN XY: 74300

African (AFR) AF: 0.240 AC: 9925 AN: 41428

American (AMR) AF: 0.330 AC: 5034 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1699 AN: 5180

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4446 AN: 10570

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29957 AN: 67952

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.254 Hom.: 622

Bravo AF: 0.347

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-0.071
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1867749; hg19: chr2-120013912; COSMIC: COSV61528344;