dbSNP rs10759637: SLC31A1:c.*2271A>C (chr9-113262744-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001859.4(SLC31A1):c.*2271A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,490 control chromosomes in the GnomAD database, including 17,438 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 0.47 ( 17384 hom., cov: 33)

Exomes 𝑓: 0.50 ( 54 hom. )

Consequence

SLC31A1
NM_001859.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.565

Publications

11 publications found

Variant links:

Genes affected

SLC31A1 (HGNC:11016): (solute carrier family 31 member 1) The protein encoded by this gene is a high-affinity copper transporter found in the cell membrane. The encoded protein functions as a homotrimer to effect the uptake of dietary copper. [provided by RefSeq, Aug 2011]

SLC31A1 links:

CDC26 (HGNC:17839): (cell division cycle 26) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Cdc26, a component of cell cycle anaphase-promoting complex (APC). APC is composed of a group of highly conserved proteins and functions as a cell cycle-regulated ubiquitin-protein ligase. APC thus is responsible for the cell cycle regulated proteolysis of various proteins. [provided by RefSeq, Jul 2008]

CDC26 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001859.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC31A1	NM_001859.4	MANE Select	c.*2271A>C		3_prime_UTR	Exon 5 of 5	NP_001850.1	O15431

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC31A1	ENST00000374212.5	TSL:1 MANE Select	c.*2271A>C		3_prime_UTR	Exon 5 of 5	ENSP00000363329.4	O15431
	CDC26	ENST00000490408.5	TSL:3	n.401-6196T>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71881

AN:

151946

Hom.:

17368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.488

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.527

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.498

AC:

212

AN:

426

Hom.:

Cov.:

AF XY:

0.511

AC XY:

134

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.498

AC:

203

AN:

408

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.583

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.473

AC:

71950

AN:

152064

Hom.:

17384

Cov.:

AF XY:

0.477

AC XY:

35435

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.541

AC:

22448

AN:

41480

American (AMR)

AF:

0.417

AC:

6360

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.527

AC:

1828

AN:

3470

East Asian (EAS)

AF:

0.481

AC:

2484

AN:

5166

South Asian (SAS)

AF:

0.588

AC:

2840

AN:

4826

European-Finnish (FIN)

AF:

0.474

AC:

5012

AN:

10572

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.433

AC:

29460

AN:

67964

Other (OTH)

AF:

0.451

AC:

954

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1977

3954

5930

7907

9884

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.448

Hom.:

36572

Bravo

AF:

0.473

Asia WGS

AF:

0.565

AC:

1960

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.0

(source)

DANN

Benign

0.37

PhyloP100

0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over