rs3116150

Variant names:

• chr16-31486700-G-A
• rs3116150
• NM_003041.4:c.574+425G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003041.4(SLC5A2):​c.574+425G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,194 control chromosomes in the GnomAD database, including 2,999 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 0.18 (2999 hom., cov: 32)
• Consequence: SLC5A2 NM_003041.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 16 publications found

Genes affected

SLC5A2 (HGNC:11037): (solute carrier family 5 member 2) This gene encodes a member of the sodium glucose cotransporter family which are sodium-dependent glucose transport proteins. The encoded protein is the major cotransporter involved in glucose reabsorption in the kidney. Mutations in this gene are associated with renal glucosuria. Two transcript variants, one protein-coding and one not, have been found for this gene. [provided by RefSeq, Feb 2015]

SLC5A2 Gene-Disease associations (from GenCC):

• familial renal glucosuria

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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 = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A2	NM_003041.4	c.574+425G>A		intron_variant	Intron 5 of 13	ENST00000330498.4	NP_003032.1
SLC5A2	NR_130783.2	n.588+425G>A		intron_variant	Intron 5 of 11
SLC5A2	XM_006721072.5	c.574+425G>A		intron_variant	Intron 5 of 12		XP_006721135.3
SLC5A2	XM_024450402.2	c.574+425G>A		intron_variant	Intron 5 of 10		XP_024306170.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A2	ENST00000330498.4	c.574+425G>A		intron_variant	Intron 5 of 13	1	NM_003041.4	ENSP00000327943.3
SLC5A2	ENST00000419665.6	n.574+425G>A		intron_variant	Intron 5 of 11	1		ENSP00000410601.2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26918 AN: 152076 Hom.: 2999 Cov.: 32

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.218

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.177 AC: 26917 AN: 152194 Hom.: 2999 Cov.: 32 AF XY: 0.175 AC XY: 12993 AN XY: 74412

African (AFR) AF: 0.0692 AC: 2875 AN: 41540

American (AMR) AF: 0.180 AC: 2751 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5172

South Asian (SAS) AF: 0.100 AC: 483 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10584

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16784 AN: 67988

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.219 Hom.: 6510

Bravo AF: 0.172

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.68
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3116150; hg19: chr16-31498021;