NM_001042.3:c.-192C>A

Variant names:

• chr17-7281743-C-A
• rs5417
• NM_001042.3:c.-192C>A

Variant summary

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

The NM_001042.3(SLC2A4):​c.-192C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 644,948 control chromosomes in the GnomAD database, including 99,019 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 0.49 (19809 hom., cov: 33)
  • Exomes 𝑓: 0.56 (79210 hom.)
• Consequence: SLC2A4 NM_001042.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 45 publications found

Genes affected

SLC2A4 (HGNC:11009): (solute carrier family 2 member 4) This gene is a member of the solute carrier family 2 (facilitated glucose transporter) family and encodes a protein that functions as an insulin-regulated facilitative glucose transporter. In the absence of insulin, this integral membrane protein is sequestered within the cells of muscle and adipose tissue. Within minutes of insulin stimulation, the protein moves to the cell surface and begins to transport glucose across the cell membrane. Mutations in this gene have been associated with noninsulin-dependent diabetes mellitus (NIDDM). [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A4	NM_001042.3	MANE Select	c.-192C>A		5_prime_UTR	Exon 1 of 11	NP_001033.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A4	ENST00000317370.13	TSL:1 MANE Select	c.-192C>A		5_prime_UTR	Exon 1 of 11	ENSP00000320935.8
	SLC2A4	ENST00000572485.5	TSL:1	n.-192C>A		non_coding_transcript_exon	Exon 1 of 11	ENSP00000461086.1
	SLC2A4	ENST00000572485.5	TSL:1	n.-192C>A		5_prime_UTR	Exon 1 of 11	ENSP00000461086.1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74856 AN: 151970 Hom.: 19791 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.540

GnomAD4 exome AF: 0.561 AC: 276289 AN: 492860 Hom.: 79210 Cov.: 5 AF XY: 0.564 AC XY: 147213 AN XY: 260912

African (AFR) AF: 0.284 AC: 3821 AN: 13446

American (AMR) AF: 0.490 AC: 12108 AN: 24728

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 9307 AN: 15518

East Asian (EAS) AF: 0.363 AC: 11308 AN: 31130

South Asian (SAS) AF: 0.575 AC: 29835 AN: 51892

European-Finnish (FIN) AF: 0.610 AC: 23801 AN: 39004

Middle Eastern (MID) AF: 0.613 AC: 1298 AN: 2118

European-Non Finnish (NFE) AF: 0.590 AC: 169898 AN: 287776

Other (OTH) AF: 0.547 AC: 14913 AN: 27248

GnomAD4 genome AF: 0.493 AC: 74913 AN: 152088 Hom.: 19809 Cov.: 33 AF XY: 0.497 AC XY: 36953 AN XY: 74362

African (AFR) AF: 0.290 AC: 12053 AN: 41500

American (AMR) AF: 0.526 AC: 8046 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2046 AN: 3464

East Asian (EAS) AF: 0.376 AC: 1931 AN: 5140

South Asian (SAS) AF: 0.562 AC: 2711 AN: 4824

European-Finnish (FIN) AF: 0.622 AC: 6593 AN: 10596

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39695 AN: 67952

Other (OTH) AF: 0.546 AC: 1155 AN: 2116

Alfa AF: 0.558 Hom.: 62475

Bravo AF: 0.473

Asia WGS AF: 0.481 AC: 1672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		0.35
PromoterAI		-0.0015	Neutral
Mutation Taster		=299/1	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: rs5417; hg19: chr17-7185062;