Variant 22-32043287-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000343.4(SLC5A1):c.6C>T(p.Asp2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,614,004 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 37 hom., cov: 32)

Exomes 𝑓: 0.011 ( 226 hom. )

Consequence

SLC5A1
NM_000343.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.51

Variant links:

Genes affected

SLC5A1 (HGNC:11036): (solute carrier family 5 member 1) This gene encodes a member of the sodium-dependent glucose transporter (SGLT) family. The encoded integral membrane protein is the primary mediator of dietary glucose and galactose uptake from the intestinal lumen. Mutations in this gene have been associated with glucose-galactose malabsorption. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

SLC5A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 22-32043287-C-T is Benign according to our data. Variant chr22-32043287-C-T is described in ClinVar as [Benign]. Clinvar id is 341234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.51 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC5A1	NM_000343.4 linkuse as main transcript	c.6C>T	p.Asp2=	synonymous_variant	1/15	ENST00000266088.9
SLC5A1	XM_011530331.2 linkuse as main transcript	c.6C>T	p.Asp2=	synonymous_variant	1/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC5A1	ENST00000266088.9 linkuse as main transcript	c.6C>T	p.Asp2=	synonymous_variant	1/15	1	NM_000343.4	P1	P13866-1

Frequencies

GnomAD3 genomes

AF:

0.0117

AC:

1775

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00292

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0502

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00559

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00939

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.0178

AC:

4470

AN:

250554

Hom.:

137

AF XY:

0.0152

AC XY:

2066

AN XY:

135530

show subpopulations

Gnomad AFR exome

AF:

0.00284

Gnomad AMR exome

AF:

0.0796

Gnomad ASJ exome

AF:

0.0300

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00434

Gnomad FIN exome

AF:

0.00362

Gnomad NFE exome

AF:

0.00944

Gnomad OTH exome

AF:

0.0149

GnomAD4 exome

AF:

0.0114

AC:

16647

AN:

1461648

Hom.:

226

Cov.:

AF XY:

0.0109

AC XY:

7893

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.00194

Gnomad4 AMR exome

AF:

0.0769

Gnomad4 ASJ exome

AF:

0.0284

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00464

Gnomad4 FIN exome

AF:

0.00387

Gnomad4 NFE exome

AF:

0.00997

Gnomad4 OTH exome

AF:

0.0113

GnomAD4 genome

AF:

0.0117

AC:

1782

AN:

152356

Hom.:

Cov.:

AF XY:

0.0114

AC XY:

847

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00291

Gnomad4 AMR

AF:

0.0508

Gnomad4 ASJ

AF:

0.0308

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.00424

Gnomad4 NFE

AF:

0.00938

Gnomad4 OTH

AF:

0.0208

Alfa

AF:

0.0114

Hom.:

Bravo

AF:

0.0154

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.00867

EpiControl

AF:

0.00836

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital glucose-galactose malabsorption

Benign:3

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 11, 2021	- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.3

DANN

Benign

0.97

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