22-32086334-T-G

Variant names:

• chr22-32086334-T-G
• rs5998233
• NM_000343.4:c.1129+7T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000343.4(SLC5A1):​c.1129+7T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,588,556 control chromosomes in the GnomAD database, including 131,733 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.48 (20763 hom., cov: 31)
  • Exomes 𝑓: 0.38 (110970 hom.)
• Consequence: SLC5A1 NM_000343.4 splice_region, intron
• Scores: Splicing: ADA: 0.00002167
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.979

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]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 22-32086334-T-G is Benign according to our data. Variant chr22-32086334-T-G is described in ClinVar as [Benign]. Clinvar id is 341249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-32086334-T-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A1	NM_000343.4	c.1129+7T>G		splice_region_variant, intron_variant	Intron 10 of 14	ENST00000266088.9	NP_000334.1
SLC5A1	NM_001256314.2	c.748+7T>G		splice_region_variant, intron_variant	Intron 9 of 13		NP_001243243.1
SLC5A1	XM_011530331.2	c.1129+7T>G		splice_region_variant, intron_variant	Intron 10 of 11		XP_011528633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A1	ENST00000266088.9	c.1129+7T>G		splice_region_variant, intron_variant	Intron 10 of 14	1	NM_000343.4	ENSP00000266088.4
SLC5A1	ENST00000543737.2	c.748+7T>G		splice_region_variant, intron_variant	Intron 9 of 13	2		ENSP00000444898.1
SLC5A1	ENST00000477969.1	n.295+7T>G		splice_region_variant, intron_variant	Intron 2 of 4	3
SLC5A1	ENST00000486394.1	n.*8T>G		downstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72305 AN: 151838 Hom.: 20709 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.425

GnomAD2 exomes AF: 0.362 AC: 90985 AN: 251372 AF XY: 0.359

Gnomad AFR exome AF: 0.827

Gnomad AMR exome AF: 0.274

Gnomad ASJ exome AF: 0.386

Gnomad EAS exome AF: 0.164

Gnomad FIN exome AF: 0.274

Gnomad NFE exome AF: 0.367

Gnomad OTH exome AF: 0.344

GnomAD4 exome AF: 0.382 AC: 548795 AN: 1436600 Hom.: 110970 Cov.: 25 AF XY: 0.380 AC XY: 272334 AN XY: 716406

Gnomad4 AFR exome AF: 0.839 AC: 27712 AN: 33038

Gnomad4 AMR exome AF: 0.278 AC: 12441 AN: 44694

Gnomad4 ASJ exome AF: 0.384 AC: 9967 AN: 25950

Gnomad4 EAS exome AF: 0.151 AC: 5972 AN: 39544

Gnomad4 SAS exome AF: 0.378 AC: 32432 AN: 85842

Gnomad4 FIN exome AF: 0.282 AC: 15057 AN: 53318

Gnomad4 NFE exome AF: 0.385 AC: 419676 AN: 1089012

Gnomad4 Remaining exome AF: 0.393 AC: 23379 AN: 59484

GnomAD4 genome AF: 0.477 AC: 72421 AN: 151956 Hom.: 20763 Cov.: 31 AF XY: 0.466 AC XY: 34580 AN XY: 74278

Gnomad4 AFR AF: 0.815 AC: 0.815286 AN: 0.815286

Gnomad4 AMR AF: 0.346 AC: 0.345917 AN: 0.345917

Gnomad4 ASJ AF: 0.396 AC: 0.395677 AN: 0.395677

Gnomad4 EAS AF: 0.157 AC: 0.157193 AN: 0.157193

Gnomad4 SAS AF: 0.375 AC: 0.374637 AN: 0.374637

Gnomad4 FIN AF: 0.278 AC: 0.278419 AN: 0.278419

Gnomad4 NFE AF: 0.369 AC: 0.369042 AN: 0.369042

Gnomad4 OTH AF: 0.426 AC: 0.425592 AN: 0.425592

Alfa AF: 0.415 Hom.: 6730

Bravo AF: 0.494

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Congenital glucose-galactose malabsorption Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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	-0.83
CADD	Benign	0.84
DANN	Benign	0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000022
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs5998233; hg19: chr22-32482321; COSMIC: COSV56688825; COSMIC: COSV56688825;