dbSNP rs838072: STEAP3:c.1215+2561A>G (chr2-119257409-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182915.3(STEAP3):c.1215+2561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 1,417,668 control chromosomes in the GnomAD database, including 639,100 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 0.95 ( 69115 hom., cov: 31)

Exomes 𝑓: 0.95 ( 569985 hom. )

Consequence

STEAP3
NM_182915.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.711

Publications

7 publications found

Variant links:

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 links:

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

STEAP3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP3	NM_182915.3 link	c.1215+2561A>G		intron_variant	Intron 5 of 5	ENST00000393110.7	NP_878919.2	Q658P3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP3	ENST00000393110.7 link	c.1215+2561A>G		intron_variant	Intron 5 of 5	1	NM_182915.3	ENSP00000376822.2		Q658P3-2

Frequencies

GnomAD3 genomes

AF:

0.953

AC:

144905

AN:

152118

Hom.:

69058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.958

Gnomad AMI

AF:

0.930

Gnomad AMR

AF:

0.964

Gnomad ASJ

AF:

0.931

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.983

Gnomad FIN

AF:

0.948

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.943

Gnomad OTH

AF:

0.942

GnomAD2 exomes

AF:

0.957

AC:

53430

AN:

55812

AF XY:

0.957

show subpopulations

Gnomad AFR exome

AF:

0.965

Gnomad AMR exome

AF:

0.974

Gnomad ASJ exome

AF:

0.939

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.946

Gnomad NFE exome

AF:

0.946

Gnomad OTH exome

AF:

0.958

GnomAD4 exome

AF:

0.949

AC:

1200952

AN:

1265432

Hom.:

569985

Cov.:

AF XY:

0.950

AC XY:

581907

AN XY:

612526

show subpopulations

African (AFR)

AF:

0.960

AC:

25325

AN:

26368

American (AMR)

AF:

0.968

AC:

16231

AN:

16770

Ashkenazi Jewish (ASJ)

AF:

0.939

AC:

17814

AN:

18970

East Asian (EAS)

AF:

1.00

AC:

29673

AN:

29676

South Asian (SAS)

AF:

0.986

AC:

55998

AN:

56804

European-Finnish (FIN)

AF:

0.946

AC:

42041

AN:

44452

Middle Eastern (MID)

AF:

0.960

AC:

4963

AN:

5170

European-Non Finnish (NFE)

AF:

0.945

AC:

959083

AN:

1015094

Other (OTH)

AF:

0.956

AC:

49824

AN:

52128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

2998

5996

8995

11993

14991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20900

41800

62700

83600

104500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.953

AC:

145019

AN:

152236

Hom.:

69115

Cov.:

AF XY:

0.955

AC XY:

71054

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.958

AC:

39780

AN:

41534

American (AMR)

AF:

0.964

AC:

14752

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.931

AC:

3234

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5168

AN:

5170

South Asian (SAS)

AF:

0.984

AC:

4743

AN:

4822

European-Finnish (FIN)

AF:

0.948

AC:

10050

AN:

10600

Middle Eastern (MID)

AF:

0.956

AC:

281

AN:

294

European-Non Finnish (NFE)

AF:

0.943

AC:

64170

AN:

68020

Other (OTH)

AF:

0.943

AC:

1993

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

358

715

1073

1430

1788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.947

Hom.:

120126

Bravo

AF:

0.954

Asia WGS

AF:

0.991

AC:

3447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.4

(source)

DANN

Benign

0.63

PhyloP100

-0.71

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over