rs6720040

Variant names:

• chr2-119261955-A-C
• rs6720040
• NM_182915.3:c.1216-1102A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-119261955-A-C
• chr2-119261955-A-G
• chr2-119261955-A-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.1216-1102A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,008 control chromosomes in the GnomAD database, including 25,014 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 0.57 (25014 hom., cov: 32)
• Consequence: STEAP3 NM_182915.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP3	NM_182915.3	c.1216-1102A>C		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.1216-1102A>C		intron_variant	Intron 5 of 5	1	NM_182915.3	ENSP00000376822.2

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86605 AN: 151890 Hom.: 25002 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.570 AC: 86644 AN: 152008 Hom.: 25014 Cov.: 32 AF XY: 0.565 AC XY: 42013 AN XY: 74306

African (AFR) AF: 0.564 AC: 23387 AN: 41436

American (AMR) AF: 0.477 AC: 7290 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2048 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1771 AN: 5134

South Asian (SAS) AF: 0.441 AC: 2128 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6401 AN: 10582

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41726 AN: 67974

Other (OTH) AF: 0.610 AC: 1286 AN: 2108

Alfa AF: 0.584 Hom.: 6524

Bravo AF: 0.558

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.50
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: rs6720040; hg19: chr2-120019531; COSMIC: COSV61528364;