Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005847.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A1	NM_005847.5	MANE Select	c.1074-101C>T		intron	N/A	NP_005838.3
	SLC23A1	NM_152685.4		c.1086-101C>T		intron	N/A	NP_689898.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC23A1	ENST00000348729.8	TSL:1 MANE Select	c.1074-101C>T	intron	N/A	ENSP00000302701.4
SLC23A1	ENST00000353963.7	TSL:1	c.1086-101C>T	intron	N/A	ENSP00000302851.5
SLC23A1	ENST00000504513.1	TSL:5	c.312-101C>T	intron	N/A	ENSP00000422688.1

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 v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over