4-10054752-T-C

Variant names:

• chr4-10054752-T-C
• rs7671266
• ENST00000506583.5:c.-176+81A>G

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-176+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,152 control chromosomes in the GnomAD database, including 41,580 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 0.73 (41576 hom., cov: 33)
  • Exomes 𝑓: 0.60 (4 hom.)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 25 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-176+81A>G		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+81A>G		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-1107T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111276 AN: 152014 Hom.: 41545 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.732

GnomAD4 exome AF: 0.600 AC: 12 AN: 20 Hom.: 4 AF XY: 0.750 AC XY: 12 AN XY: 16

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: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.643 AC: 9 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.732 AC: 111358 AN: 152132 Hom.: 41576 Cov.: 33 AF XY: 0.735 AC XY: 54675 AN XY: 74362

African (AFR) AF: 0.581 AC: 24072 AN: 41466

American (AMR) AF: 0.722 AC: 11040 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5061 AN: 5180

South Asian (SAS) AF: 0.808 AC: 3902 AN: 4828

European-Finnish (FIN) AF: 0.820 AC: 8679 AN: 10588

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.789 AC: 53639 AN: 67996

Other (OTH) AF: 0.735 AC: 1547 AN: 2106

Alfa AF: 0.771 Hom.: 140870

Bravo AF: 0.717

Asia WGS AF: 0.882 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.76
PhyloP100		-1.2
PromoterAI		0.0091	Neutral
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: rs7671266; hg19: chr4-10056376;