16-31484350-G-C

Position:

• chr16-31484350-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003041.4(SLC5A2):​c.127-323G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,188 control chromosomes in the GnomAD database, including 10,299 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.33 (10299 hom., cov: 28)
• Consequence: SLC5A2 NM_003041.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 16-31484350-G-C is Benign according to our data. Variant chr16-31484350-G-C is described in ClinVar as [Benign]. Clinvar id is 1241803.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC5A2	NM_003041.4	c.127-323G>C		intron_variant		ENST00000330498.4
SLC5A2	XM_006721072.5	c.127-323G>C		intron_variant
SLC5A2	XM_024450402.2	c.127-323G>C		intron_variant
SLC5A2	NR_130783.2	n.141-323G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC5A2	ENST00000330498.4	c.127-323G>C		intron_variant		1	NM_003041.4	P1
SLC5A2	ENST00000419665.6	c.127-323G>C		intron_variant, NMD_transcript_variant		1
SLC5A2	ENST00000569576.5	c.-3-323G>C		intron_variant		4
SLC5A2	ENST00000562006.1	n.126-323G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50532 AN: 151070 Hom.: 10294 Cov.: 28

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.334 AC: 50540 AN: 151188 Hom.: 10299 Cov.: 28 AF XY: 0.334 AC XY: 24646 AN XY: 73748

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.408

Alfa AF: 0.236 Hom.: 614

Bravo AF: 0.343

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.52

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; COSMIC: COSV57893572; COSMIC: COSV57893572;