12-39835220-T-G

Position:

• chr12-39835220-T-G

Variant summary

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

The NM_052885.4(SLC2A13):​c.1320-4992A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,974 control chromosomes in the GnomAD database, including 5,945 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 0.27 (5945 hom., cov: 31)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

SLC2A13 (HGNC:15956): (solute carrier family 2 member 13) Enables ATPase binding activity; myo-inositol:proton symporter activity; and protease binding activity. Involved in myo-inositol transport and positive regulation of amyloid-beta formation. Is integral component of plasma membrane. Part of cell body; cell periphery; and cell projection. [provided by Alliance of Genome Resources, Apr 2022]

C12orf40 (HGNC:26846): (regulator of DNA class I crossover intermediates 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A13	NM_052885.4	c.1320-4992A>C		intron_variant		ENST00000280871.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A13	ENST00000280871.9	c.1320-4992A>C		intron_variant		1	NM_052885.4	P1
C12orf40	ENST00000468200.2	c.*998+32838T>G		intron_variant, NMD_transcript_variant		1
SLC2A13	ENST00000465517.1	n.206-4992A>C		intron_variant, non_coding_transcript_variant		2
SLC2A13	ENST00000505338.1	n.80+461A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40745 AN: 151856 Hom.: 5946 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.268 AC: 40757 AN: 151974 Hom.: 5945 Cov.: 31 AF XY: 0.267 AC XY: 19864 AN XY: 74292

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.296

Alfa AF: 0.298 Hom.: 6617

Bravo AF: 0.282

Asia WGS AF: 0.309 AC: 1072 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.74

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: rs7963790; hg19: chr12-40229022;