rs1342809

Variant names:

• chr1-192801422-G-T
• rs1342809
• ENST00000644058.1:n.194-35228C>A

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.194-35228C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,118 control chromosomes in the GnomAD database, including 1,387 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 0.12 (1387 hom., cov: 33)
• Consequence: ENSG00000285280 ENST00000644058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 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 (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000644058.1	n.194-35228C>A		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-35228C>A		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-8954C>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17905 AN: 152000 Hom.: 1386 Cov.: 33

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.118 AC: 17900 AN: 152118 Hom.: 1387 Cov.: 33 AF XY: 0.113 AC XY: 8386 AN XY: 74372

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0513

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.139

Alfa AF: 0.126 Hom.: 209

Bravo AF: 0.118

Asia WGS AF: 0.0650 AC: 229 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342809; hg19: chr1-192770552;