dbSNP rs11950646: SLC23A1:c.1074-101C>T (chr5-139378785-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005847.5(SLC23A1):c.1074-101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 841,620 control chromosomes in the GnomAD database, including 155,389 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 0.48 ( 21694 hom., cov: 31)

Exomes 𝑓: 0.61 ( 133695 hom. )

Consequence

SLC23A1
NM_005847.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Publications

28 publications found

Variant links:

Genes affected

SLC23A1 (HGNC:10974): (solute carrier family 23 member 1) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

SLC23A1 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A1	NM_005847.5 link	c.1074-101C>T		intron_variant	Intron 9 of 14	ENST00000348729.8	NP_005838.3	Q9UHI7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC23A1	ENST00000348729.8 link	c.1074-101C>T	intron_variant	Intron 9 of 14	1	NM_005847.5	ENSP00000302701.4	Q9UHI7-1
SLC23A1	ENST00000353963.7 link	c.1086-101C>T	intron_variant	Intron 9 of 14	1		ENSP00000302851.5	Q9UHI7-2
SLC23A1	ENST00000504513.1 link	c.312-101C>T	intron_variant	Intron 3 of 3	5		ENSP00000422688.1	H0Y902

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73444

AN:

151898

Hom.:

21702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.659

Gnomad OTH

AF:

0.505

GnomAD4 exome

AF:

0.610

AC:

420883

AN:

689602

Hom.:

133695

AF XY:

0.610

AC XY:

220508

AN XY:

361490

show subpopulations

African (AFR)

AF:

0.145

AC:

2656

AN:

18300

American (AMR)

AF:

0.609

AC:

20032

AN:

32900

Ashkenazi Jewish (ASJ)

AF:

0.527

AC:

9942

AN:

18882

East Asian (EAS)

AF:

0.323

AC:

10526

AN:

32628

South Asian (SAS)

AF:

0.554

AC:

34052

AN:

61476

European-Finnish (FIN)

AF:

0.666

AC:

30799

AN:

46236

Middle Eastern (MID)

AF:

0.530

AC:

2264

AN:

4270

European-Non Finnish (NFE)

AF:

0.661

AC:

291118

AN:

440268

Other (OTH)

AF:

0.563

AC:

19494

AN:

34642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

8203

16406

24610

32813

41016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3888

7776

11664

15552

19440

<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:

0.483

AC:

73440

AN:

152018

Hom.:

21694

Cov.:

AF XY:

0.482

AC XY:

35823

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.140

AC:

5792

AN:

41498

American (AMR)

AF:

0.539

AC:

8224

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1848

AN:

3470

East Asian (EAS)

AF:

0.279

AC:

1441

AN:

5166

South Asian (SAS)

AF:

0.543

AC:

2611

AN:

4810

European-Finnish (FIN)

AF:

0.663

AC:

7005

AN:

10564

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.659

AC:

44771

AN:

67936

Other (OTH)

AF:

0.502

AC:

1058

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1514

3028

4543

6057

7571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.600

Hom.:

72572

Bravo

AF:

0.462

Asia WGS

AF:

0.387

AC:

1346

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.7

(source)

DANN

Benign

0.78

PhyloP100

0.033

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over