4-10034715-A-G

Variant names:

• chr4-10034715-A-G
• rs3733585
• ENST00000309065.7:c.-41+5415T>C

Variant summary

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

The ENST00000309065.7(SLC2A9):​c.-41+5415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,084 control chromosomes in the GnomAD database, including 16,143 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 0.44 (16132 hom., cov: 32)
  • Exomes 𝑓: 0.57 (11 hom.)
• Consequence: SLC2A9 ENST00000309065.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 19 publications found

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]

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000309065.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_001001290.2		c.-41+5415T>C		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000309065.7	TSL:1	c.-41+5415T>C		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.81+5415T>C		intron	N/A
	SLC2A9	ENST00000481042.1	TSL:2	n.1685T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66457 AN: 151906 Hom.: 16123 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.449

GnomAD4 exome AF: 0.567 AC: 34 AN: 60 Hom.: 11 Cov.: 0 AF XY: 0.525 AC XY: 21 AN XY: 40

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.540 AC: 27 AN: 50

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.437 AC: 66477 AN: 152024 Hom.: 16132 Cov.: 32 AF XY: 0.439 AC XY: 32657 AN XY: 74310

African (AFR) AF: 0.206 AC: 8557 AN: 41484

American (AMR) AF: 0.486 AC: 7424 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2195 AN: 5168

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5521 AN: 10576

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36523 AN: 67932

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.502 Hom.: 15080

Bravo AF: 0.423

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.46
PhyloP100		0.033
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3733585; hg19: chr4-10036339;