12-39880800-G-T

Variant names:

• chr12-39880800-G-T
• rs10877703
• NM_052885.4:c.1035-8839C>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.1035-8839C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,020 control chromosomes in the GnomAD database, including 5,445 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 0.26 (5445 hom., cov: 32)
• Consequence: SLC2A13 NM_052885.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A13	NM_052885.4	c.1035-8839C>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.1035-8839C>A		intron_variant	Intron 4 of 9	1	NM_052885.4	ENSP00000280871.4
REDIC1	ENST00000468200.2	n.*999-26834G>T		intron_variant	Intron 18 of 18	1		ENSP00000473371.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39573 AN: 151902 Hom.: 5443 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.260 AC: 39590 AN: 152020 Hom.: 5445 Cov.: 32 AF XY: 0.259 AC XY: 19241 AN XY: 74306

African (AFR) AF: 0.173 AC: 7193 AN: 41484

American (AMR) AF: 0.354 AC: 5406 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2051 AN: 5162

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4814

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10554

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

European-Non Finnish (NFE) AF: 0.284 AC: 19284 AN: 67934

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.248 Hom.: 2036

Bravo AF: 0.275

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.64
PhyloP100		-1.6
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: rs10877703; hg19: chr12-40274602;