rs2032893

Variant names:

• chr5-36698520-C-T
• rs2032893
• ENST00000510740.2:n.105+26594G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510740.2(SLC1A3-AS1):​n.105+26594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,008 control chromosomes in the GnomAD database, including 11,792 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 0.39 (11792 hom., cov: 32)
• Consequence: SLC1A3-AS1 ENST00000510740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 3 publications found

Genes affected

SLC1A3-AS1 (HGNC:56374): (SLC1A3 antisense RNA 1)

ENSG00000297819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A3-AS1	XR_007058736.1	n.75+26594G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A3-AS1	ENST00000510740.2	n.105+26594G>A		intron_variant	Intron 1 of 2	3
SLC1A3-AS1	ENST00000750858.1	n.263+7160G>A		intron_variant	Intron 2 of 3
SLC1A3-AS1	ENST00000750859.1	n.91+26594G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59400 AN: 151890 Hom.: 11781 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.391 AC: 59445 AN: 152008 Hom.: 11792 Cov.: 32 AF XY: 0.390 AC XY: 28987 AN XY: 74284

African (AFR) AF: 0.388 AC: 16080 AN: 41438

American (AMR) AF: 0.349 AC: 5339 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2515 AN: 5158

South Asian (SAS) AF: 0.478 AC: 2305 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3674 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26772 AN: 67962

Other (OTH) AF: 0.374 AC: 788 AN: 2108

Alfa AF: 0.384 Hom.: 1416

Bravo AF: 0.389

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.19
PhyloP100		-0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2032893; hg19: chr5-36698622;