3-171006421-C-T

Position:

• chr3-171006421-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000340.2(SLC2A2):​c.613-316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,072 control chromosomes in the GnomAD database, including 175 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 0.047 (175 hom., cov: 32)
• Consequence: SLC2A2 NM_000340.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

Genes affected

SLC2A2 (HGNC:11006): (solute carrier family 2 member 2) This gene encodes an integral plasma membrane glycoprotein of the liver, islet beta cells, intestine, and kidney epithelium. The encoded protein mediates facilitated bidirectional glucose transport. Because of its low affinity for glucose, it has been suggested as a glucose sensor. Mutations in this gene are associated with susceptibility to diseases, including Fanconi-Bickel syndrome and noninsulin-dependent diabetes mellitus (NIDDM). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0466 (7094/152072) while in subpopulation NFE AF= 0.0492 (3342/67930). AF 95% confidence interval is 0.0478. There are 175 homozygotes in gnomad4. There are 3531 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 175 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A2	NM_000340.2	c.613-316G>A		intron_variant		ENST00000314251.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A2	ENST00000314251.8	c.613-316G>A		intron_variant		1	NM_000340.2	P1
	ENST00000655926.1	n.291+11396C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0467 AC: 7092 AN: 151954 Hom.: 175 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0466 AC: 7094 AN: 152072 Hom.: 175 Cov.: 32 AF XY: 0.0475 AC XY: 3531 AN XY: 74336

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.0462

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0502 Hom.: 102

Bravo AF: 0.0435

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.063
DANN	Benign	0.48

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: rs10513684; hg19: chr3-170724210;