Genetic Variant NM_030777.4:c.1547+18T>G (chr20-46729506-T-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030777.4(SLC2A10):c.1547+18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,611,072 control chromosomes in the GnomAD database, including 141,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11570 hom., cov: 31)

Exomes 𝑓: 0.42 ( 130285 hom. )

Consequence

SLC2A10
NM_030777.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -2.87

Variant links:

Genes affected

SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]

SLC2A10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 20-46729506-T-G is Benign according to our data. Variant chr20-46729506-T-G is described in ClinVar as [Benign]. Clinvar id is 139178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-46729506-T-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A10	NM_030777.4 link	c.1547+18T>G		intron_variant	Intron 4 of 4	ENST00000359271.4	NP_110404.1	O95528

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4 link	c.1547+18T>G		intron_variant	Intron 4 of 4	1	NM_030777.4	ENSP00000352216.2		O95528

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

56918

AN:

151560

Hom.:

11559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.459

Gnomad MID

AF:

0.359

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.406

GnomAD3 exomes

AF:

0.418

AC:

104878

AN:

250922

Hom.:

22616

AF XY:

0.417

AC XY:

56542

AN XY:

135740

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.422

Gnomad ASJ exome

AF:

0.440

Gnomad EAS exome

AF:

0.607

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.449

Gnomad NFE exome

AF:

0.426

Gnomad OTH exome

AF:

0.420

GnomAD4 exome

AF:

0.418

AC:

610606

AN:

1459404

Hom.:

130285

Cov.:

AF XY:

0.416

AC XY:

302134

AN XY:

726134

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.423

Gnomad4 ASJ exome

AF:

0.435

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.346

Gnomad4 FIN exome

AF:

0.443

Gnomad4 NFE exome

AF:

0.422

Gnomad4 OTH exome

AF:

0.416

GnomAD4 genome

AF:

0.376

AC:

56954

AN:

151668

Hom.:

11570

Cov.:

AF XY:

0.380

AC XY:

28180

AN XY:

74064

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.599

Gnomad4 SAS

AF:

0.341

Gnomad4 FIN

AF:

0.459

Gnomad4 NFE

AF:

0.424

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.327

Hom.:

1477

Bravo

AF:

0.370

Asia WGS

AF:

0.426

AC:

1478

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 12, 2019

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: SLC2A10 c.1547+18T>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.42 in 250922 control chromosomes, predominantly at a frequency of 0.61 within the East Asian subpopulation in the gnomAD database, including 3377 homozygotes. Therefore, suggesting the variant is the major allele found in population(s) of East Asian origin. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -

Nov 20, 2012

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Arterial tortuosity syndrome

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.027

DANN

Benign

0.58

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over