chr4-10011549-T-G

Position:

• chr4-10011549-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020041.3(SLC2A9):​c.249+7426A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,172 control chromosomes in the GnomAD database, including 24,211 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 0.56 (24211 hom., cov: 34)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

LOC124900664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.249+7426A>C		intron_variant		ENST00000264784.8	NP_064425.2
LOC124900664	XR_007058024.1	n.2285T>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.249+7426A>C		intron_variant		1	NM_020041.3	ENSP00000264784	A2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84385 AN: 152054 Hom.: 24180 Cov.: 34

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.555 AC: 84463 AN: 152172 Hom.: 24211 Cov.: 34 AF XY: 0.562 AC XY: 41781 AN XY: 74378

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.561

Alfa AF: 0.580 Hom.: 11834

Bravo AF: 0.549

Asia WGS AF: 0.789 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
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: rs6845554; hg19: chr4-10013173;