rs1557770

Variant names:

• chrX-115560848-T-G
• rs1557770
• ENST00000606397.1:n.209+1556A>C

Variant summary

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

The ENST00000607680.5(PLS3-AS1):​n.233+1556A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 111,250 control chromosomes in the GnomAD database, including 9,106 homozygotes. There are 15,765 hemizygotes in GnomAD. 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 0.47 (9106 hom., 15765 hem., cov: 24)
• Consequence: PLS3-AS1 ENST00000607680.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

Genes affected

PLS3-AS1 (HGNC:50343): (PLS3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLS3-AS1	NR_110383.1	n.233+1556A>C		intron_variant	Intron 2 of 4
PLS3-AS1	NR_110384.1	n.233+1556A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLS3-AS1	ENST00000606397.1	n.209+1556A>C		intron_variant	Intron 2 of 3	4
PLS3-AS1	ENST00000607680.5	n.233+1556A>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.465 AC: 51739 AN: 111196 Hom.: 9105 Cov.: 24 AF XY: 0.472 AC XY: 15754 AN XY: 33406

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.465 AC: 51748 AN: 111250 Hom.: 9106 Cov.: 24 AF XY: 0.471 AC XY: 15765 AN XY: 33470

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.496

Alfa AF: 0.547 Hom.: 48523

Bravo AF: 0.445

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557770; hg19: chrX-114795175;