ENST00000508745.3:n.102+5237G>A

Variant names:

• chr5-36719877-C-T
• rs6451305
• ENST00000508745.3:n.102+5237G>A

Variant summary

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

The ENST00000508745.3(SLC1A3-AS1):​n.102+5237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,150 control chromosomes in the GnomAD database, including 39,978 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 0.72 (39978 hom., cov: 33)
• Consequence: SLC1A3-AS1 ENST00000508745.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A3-AS1	XR_001742638.2	n.75+5237G>A		intron_variant	Intron 1 of 2
SLC1A3-AS1	XR_007058736.1	n.75+5237G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A3-AS1	ENST00000508745.3	n.102+5237G>A		intron_variant	Intron 1 of 2	3
SLC1A3-AS1	ENST00000510740.2	n.105+5237G>A		intron_variant	Intron 1 of 2	3
SLC1A3-AS1	ENST00000512329.3	n.75+5237G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109659 AN: 152032 Hom.: 39962 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.721 AC: 109724 AN: 152150 Hom.: 39978 Cov.: 33 AF XY: 0.722 AC XY: 53699 AN XY: 74368

African (AFR) AF: 0.621 AC: 25770 AN: 41484

American (AMR) AF: 0.787 AC: 12044 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3892 AN: 5174

South Asian (SAS) AF: 0.718 AC: 3456 AN: 4814

European-Finnish (FIN) AF: 0.748 AC: 7931 AN: 10600

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51803 AN: 67992

Other (OTH) AF: 0.716 AC: 1509 AN: 2108

Alfa AF: 0.737 Hom.: 7032

Bravo AF: 0.724

Asia WGS AF: 0.693 AC: 2410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.49
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6451305; hg19: chr5-36719979;