rs6451305

Positions:

• chr5-36719877-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510740.1(SLC1A3-AS1):​n.60+5237G>A variant causes a intron, non coding transcript 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 ENST00000510740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC1A3-AS1	XR_007058736.1	n.75+5237G>A		intron_variant, non_coding_transcript_variant
SLC1A3-AS1	XR_001742638.2	n.75+5237G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A3-AS1	ENST00000510740.1	n.60+5237G>A		intron_variant, non_coding_transcript_variant		3
SLC1A3-AS1	ENST00000508745.2	n.91+5237G>A		intron_variant, non_coding_transcript_variant		3
SLC1A3-AS1	ENST00000512329.2	n.63+5237G>A		intron_variant, non_coding_transcript_variant		3
SLC1A3-AS1	ENST00000659180.1	n.46+5237G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.716

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6451305; hg19: chr5-36719979;