chr16-31484350-G-A

Variant names:

• chr16-31484350-G-A
• rs11646054
• NM_003041.4:c.127-323G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003041.4(SLC5A2):​c.127-323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
• Consequence: SLC5A2 NM_003041.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A2	NM_003041.4	c.127-323G>A		intron_variant	Intron 1 of 13	ENST00000330498.4	NP_003032.1
SLC5A2	XM_006721072.5	c.127-323G>A		intron_variant	Intron 1 of 12		XP_006721135.3
SLC5A2	XM_024450402.2	c.127-323G>A		intron_variant	Intron 1 of 10		XP_024306170.2
SLC5A2	NR_130783.2	n.141-323G>A		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A2	ENST00000330498.4	c.127-323G>A		intron_variant	Intron 1 of 13	1	NM_003041.4	ENSP00000327943.3
SLC5A2	ENST00000419665.6	n.127-323G>A		intron_variant	Intron 1 of 11	1		ENSP00000410601.2
SLC5A2	ENST00000569576.5	c.-3-323G>A		intron_variant	Intron 1 of 4	4		ENSP00000455143.1
SLC5A2	ENST00000562006.1	n.126-323G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.39

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

Other links and lift over

dbSNP: rs11646054; hg19: chr16-31495671;