12-39835220-T-G

Variant names:

• chr12-39835220-T-G
• rs7963790
• NM_052885.4:c.1320-4992A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052885.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	NM_052885.4	MANE Select	c.1320-4992A>C		intron	N/A	NP_443117.3
	REDIC1	NR_135051.2		n.2429+32838T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A13	ENST00000280871.9	TSL:1 MANE Select	c.1320-4992A>C		intron	N/A	ENSP00000280871.4
	REDIC1	ENST00000468200.2	TSL:1	n.*998+32838T>G		intron	N/A	ENSP00000473371.1
	SLC2A13	ENST00000465517.1	TSL:2	n.206-4992A>C		intron	N/A

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

African (AFR) AF: 0.151 AC: 6286 AN: 41500

American (AMR) AF: 0.364 AC: 5549 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.444 AC: 2285 AN: 5148

South Asian (SAS) AF: 0.206 AC: 994 AN: 4824

European-Finnish (FIN) AF: 0.257 AC: 2717 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20793 AN: 67926

Other (OTH) AF: 0.296 AC: 624 AN: 2108

Alfa AF: 0.297 Hom.: 8542

Bravo AF: 0.282

Asia WGS AF: 0.309 AC: 1072 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.74
PhyloP100		0.15
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: rs7963790; hg19: chr12-40229022;