1-192815708-T-C

Variant names:

• chr1-192815708-T-C
• rs1819741
• ENST00000644058.1:n.194-49514A>G

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.194-49514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,108 control chromosomes in the GnomAD database, including 5,823 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 0.27 (5823 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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.194-49514A>G		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-49514A>G		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.199+11196A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41555 AN: 151988 Hom.: 5819 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.273 AC: 41569 AN: 152108 Hom.: 5823 Cov.: 32 AF XY: 0.274 AC XY: 20365 AN XY: 74350

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.268

Alfa AF: 0.241 Hom.: 2234

Bravo AF: 0.273

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1819741; hg19: chr1-192784838;