rs2887613

Variant names:

• chr1-192925751-G-A
• rs2887613
• ENST00000644058.1:n.54C>T

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.54C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,776 control chromosomes in the GnomAD database, including 7,581 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 0.30 (7577 hom., cov: 30)
  • Exomes 𝑓: 0.21 (4 hom.)
• Consequence: ENSG00000285280 ENST00000644058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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.54C>T		non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000285280	ENST00000645822.1	n.2C>T		non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000285280	ENST00000646606.1	n.295+21562C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45751 AN: 151582 Hom.: 7571 Cov.: 30

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.211 AC: 16 AN: 76 Hom.: 4 Cov.: 0 AF XY: 0.261 AC XY: 12 AN XY: 46

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.302 AC: 45787 AN: 151700 Hom.: 7577 Cov.: 30 AF XY: 0.307 AC XY: 22720 AN XY: 74126

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.285

Alfa AF: 0.284 Hom.: 6285

Bravo AF: 0.313

Asia WGS AF: 0.518 AC: 1797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2887613; hg19: chr1-192894881;