Genetic Variant SLC35H1:c.-173G>C (chr20-46358679-C-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_015945.12(SLC35H1):c.-173G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,551,074 control chromosomes in the GnomAD database, including 70,098 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 0.24 ( 5435 hom., cov: 32)

Exomes 𝑓: 0.30 ( 64663 hom. )

Consequence

SLC35H1
NM_015945.12 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

Publications

14 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35H1	NM_015945.12 link	c.-173G>C		5_prime_UTR_variant	Exon 2 of 10	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.-173G>C		5_prime_UTR_variant	Exon 2 of 10	1	NM_015945.12	ENSP00000361304.5		Q9NQQ7-1

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

35974

AN:

152034

Hom.:

5442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0633

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.0734

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.228

GnomAD2 exomes

AF:

0.287

AC:

44249

AN:

154426

AF XY:

0.287

show subpopulations

Gnomad AFR exome

AF:

0.0517

Gnomad AMR exome

AF:

0.335

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.0688

Gnomad FIN exome

AF:

0.389

Gnomad NFE exome

AF:

0.315

Gnomad OTH exome

AF:

0.291

GnomAD4 exome

AF:

0.298

AC:

416749

AN:

1398922

Hom.:

64663

Cov.:

AF XY:

0.298

AC XY:

205526

AN XY:

689990

show subpopulations

African (AFR)

AF:

0.0522

AC:

1650

AN:

31598

American (AMR)

AF:

0.333

AC:

11900

AN:

35720

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

6200

AN:

25182

East Asian (EAS)

AF:

0.0798

AC:

2853

AN:

35738

South Asian (SAS)

AF:

0.281

AC:

22305

AN:

79278

European-Finnish (FIN)

AF:

0.380

AC:

18562

AN:

48796

Middle Eastern (MID)

AF:

0.276

AC:

1574

AN:

5698

European-Non Finnish (NFE)

AF:

0.312

AC:

336142

AN:

1078906

Other (OTH)

AF:

0.268

AC:

15563

AN:

58006

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

17693

35386

53079

70772

88465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10936

21872

32808

43744

54680

<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:

0.236

AC:

35955

AN:

152152

Hom.:

5435

Cov.:

AF XY:

0.239

AC XY:

17783

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0632

AC:

2627

AN:

41538

American (AMR)

AF:

0.276

AC:

4216

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

850

AN:

3472

East Asian (EAS)

AF:

0.0732

AC:

379

AN:

5178

South Asian (SAS)

AF:

0.269

AC:

1294

AN:

4812

European-Finnish (FIN)

AF:

0.396

AC:

4196

AN:

10584

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21422

AN:

67964

Other (OTH)

AF:

0.225

AC:

475

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1314

2628

3943

5257

6571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.210

Hom.:

789

Bravo

AF:

0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.2

(source)

DANN

Benign

0.66

PhyloP100

-0.52

PromoterAI

-0.00020

Neutral

(source)

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

SpliceAI score (max)

0.040

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