9-133475078-T-G

Position:

• chr9-133475078-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_017585.4(SLC2A6):​c.810A>C​(p.Pro270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 1,593,342 control chromosomes in the GnomAD database, including 415,396 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 0.67 (34746 hom., cov: 36)
  • Exomes 𝑓: 0.72 (380650 hom.)
• Consequence: SLC2A6 NM_017585.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

SLC2A6 (HGNC:11011): (solute carrier family 2 member 6) Hexose transport into mammalian cells is catalyzed by a family of membrane proteins, including SLC2A6, that contain 12 transmembrane domains and a number of critical conserved residues.[supplied by OMIM, Jul 2002]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP7: Synonymous conserved (PhyloP=-0.879 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A6	NM_017585.4	c.810A>C	p.Pro270=	synonymous_variant	6/10	ENST00000371899.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A6	ENST00000371899.9	c.810A>C	p.Pro270=	synonymous_variant	6/10	1	NM_017585.4	P1
SLC2A6	ENST00000371897.8	c.810A>C	p.Pro270=	synonymous_variant	6/9	2
SLC2A6	ENST00000485978.1	n.1398A>C		non_coding_transcript_exon_variant	5/8	5

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101367 AN: 152074 Hom.: 34713 Cov.: 36

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.657

GnomAD3 exomes AF: 0.730 AC: 162084 AN: 221944 Hom.: 60044 AF XY: 0.730 AC XY: 88576 AN XY: 121260

Gnomad AFR exome AF: 0.517

Gnomad AMR exome AF: 0.792

Gnomad ASJ exome AF: 0.623

Gnomad EAS exome AF: 0.934

Gnomad SAS exome AF: 0.799

Gnomad FIN exome AF: 0.680

Gnomad NFE exome AF: 0.707

Gnomad OTH exome AF: 0.706

GnomAD4 exome AF: 0.724 AC: 1043724 AN: 1441148 Hom.: 380650 Cov.: 64 AF XY: 0.726 AC XY: 519228 AN XY: 715554

Gnomad4 AFR exome AF: 0.508

Gnomad4 AMR exome AF: 0.787

Gnomad4 ASJ exome AF: 0.630

Gnomad4 EAS exome AF: 0.913

Gnomad4 SAS exome AF: 0.798

Gnomad4 FIN exome AF: 0.692

Gnomad4 NFE exome AF: 0.720

Gnomad4 OTH exome AF: 0.716

GnomAD4 genome AF: 0.667 AC: 101453 AN: 152194 Hom.: 34746 Cov.: 36 AF XY: 0.671 AC XY: 49920 AN XY: 74420

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.660

Alfa AF: 0.711 Hom.: 27921

Bravo AF: 0.662

Asia WGS AF: 0.844 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2073935; hg19: chr9-136340200; COSMIC: COSV52469587; COSMIC: COSV52469587;