12-39902938-C-T

Variant summary

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

The NM_052885.4(SLC2A13):c.1035-30977G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,822 control chromosomes in the GnomAD database, including 18,436 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 0.49 (18436 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A13	NM_052885.4	c.1035-30977G>A		intron_variant		ENST00000280871.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A13	ENST00000280871.9	c.1035-30977G>A		intron_variant		1	NM_052885.4	P1
C12orf40	ENST00000468200.2	c.*999-4696C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74309 AN: 151704 Hom.: 18427 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.490 AC: 74362 AN: 151822 Hom.: 18436 Cov.: 32 AF XY: 0.488 AC XY: 36202 AN XY: 74208

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.508

Alfa AF: 0.475 Hom.: 16896

Bravo AF: 0.510

Asia WGS AF: 0.626 AC: 2175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.037
Dann	Benign	0.34

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: rs956066; hg19: chr12-40296740;