chr5-36698520-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510740.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A3-AS1	ENST00000510740.2	TSL:3	n.105+26594G>A		intron	N/A
	SLC1A3-AS1	ENST00000750858.1		n.263+7160G>A		intron	N/A
	SLC1A3-AS1	ENST00000750859.1		n.91+26594G>A		intron	N/A

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 v4.9

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;