chr12-39902938-C-T

Variant names:

• chr12-39902938-C-T
• rs956066
• NM_052885.4:c.1035-30977G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

REDIC1 (HGNC:26846): (regulator of DNA class I crossover intermediates 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.1035-30977G>A		intron_variant	Intron 4 of 9	ENST00000280871.9	NP_443117.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A13	ENST00000280871.9	c.1035-30977G>A		intron_variant	Intron 4 of 9	1	NM_052885.4	ENSP00000280871.4
REDIC1	ENST00000468200.2	n.*999-4696C>T		intron_variant	Intron 18 of 18	1		ENSP00000473371.1

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

African (AFR) AF: 0.487 AC: 20177 AN: 41416

American (AMR) AF: 0.531 AC: 8093 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4019 AN: 5164

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4816

European-Finnish (FIN) AF: 0.358 AC: 3761 AN: 10516

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31889 AN: 67906

Other (OTH) AF: 0.508 AC: 1068 AN: 2104

Alfa AF: 0.479 Hom.: 22450

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
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs956066; hg19: chr12-40296740;