dbSNP rs12480667: SLC35H1:c.661+4C>T (chr20-46354878-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_015945.12(SLC35H1):c.661+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,592,576 control chromosomes in the GnomAD database, including 51,735 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3902 hom., cov: 32)

Exomes 𝑓: 0.25 ( 47833 hom. )

Consequence

SLC35H1
NM_015945.12 splice_region, intron

Scores

Splicing: ADA: 0.0001227

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Publications

12 publications found

Variant links:

Genes affected

SLC35H1 (HGNC:17117): (solute carrier family 35 member C2) This gene encodes a member of the triose-phosphate transporter protein family. This gene is regulated by oxygen tension, is induced in hypoxic trophoblast cells, and is overexpressed in ovarian cancer. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]

SLC35H1 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35H1	NM_015945.12 link	c.661+4C>T		splice_region_variant, intron_variant	Intron 7 of 9	ENST00000372230.10	NP_057029.8	Q9NQQ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35C2	ENST00000372230.10 link	c.661+4C>T		splice_region_variant, intron_variant	Intron 7 of 9	1	NM_015945.12	ENSP00000361304.5		Q9NQQ7-1

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30370

AN:

152046

Hom.:

3908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0511

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.0684

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.182

GnomAD2 exomes

AF:

0.234

AC:

50625

AN:

216380

AF XY:

0.234

show subpopulations

Gnomad AFR exome

AF:

0.0435

Gnomad AMR exome

AF:

0.314

Gnomad ASJ exome

AF:

0.182

Gnomad EAS exome

AF:

0.0644

Gnomad FIN exome

AF:

0.317

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.252

AC:

362726

AN:

1440412

Hom.:

47833

Cov.:

AF XY:

0.250

AC XY:

178908

AN XY:

714852

show subpopulations

African (AFR)

AF:

0.0405

AC:

1345

AN:

33226

American (AMR)

AF:

0.312

AC:

12523

AN:

40120

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

4651

AN:

25694

East Asian (EAS)

AF:

0.0754

AC:

2933

AN:

38896

South Asian (SAS)

AF:

0.199

AC:

16709

AN:

84114

European-Finnish (FIN)

AF:

0.307

AC:

15984

AN:

51994

Middle Eastern (MID)

AF:

0.195

AC:

1120

AN:

5740

European-Non Finnish (NFE)

AF:

0.267

AC:

294151

AN:

1101008

Other (OTH)

AF:

0.223

AC:

13310

AN:

59620

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

13378

26756

40134

53512

66890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9706

19412

29118

38824

48530

<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:

0.199

AC:

30351

AN:

152164

Hom.:

3902

Cov.:

AF XY:

0.201

AC XY:

14984

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0509

AC:

2117

AN:

41566

American (AMR)

AF:

0.246

AC:

3769

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

620

AN:

3470

East Asian (EAS)

AF:

0.0682

AC:

353

AN:

5178

South Asian (SAS)

AF:

0.193

AC:

930

AN:

4812

European-Finnish (FIN)

AF:

0.326

AC:

3444

AN:

10562

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18300

AN:

67964

Other (OTH)

AF:

0.179

AC:

378

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1195

2390

3586

4781

5976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<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:

0.238

Hom.:

7145

Bravo

AF:

0.187

Asia WGS

AF:

0.130

AC:

452

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.28

(source)

DANN

Benign

0.79

PhyloP100

-1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00012

dbscSNV1_RF

Benign

0.026

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