1-192827775-C-T

Variant names:

• chr1-192827775-C-T
• rs1152746
• ENST00000644058.2:n.202-61581G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644058.2(ENSG00000285280):​n.202-61581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,096 control chromosomes in the GnomAD database, including 40,242 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 0.73 (40242 hom., cov: 33)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 4 publications found

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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	ENST00000644058.2	n.202-61581G>A		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-61581G>A		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.142-814G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110332 AN: 151978 Hom.: 40206 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.726 AC: 110423 AN: 152096 Hom.: 40242 Cov.: 33 AF XY: 0.730 AC XY: 54253 AN XY: 74334

African (AFR) AF: 0.722 AC: 29968 AN: 41486

American (AMR) AF: 0.746 AC: 11396 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3470

East Asian (EAS) AF: 0.876 AC: 4546 AN: 5190

South Asian (SAS) AF: 0.813 AC: 3925 AN: 4830

European-Finnish (FIN) AF: 0.662 AC: 6991 AN: 10558

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48374 AN: 67978

Other (OTH) AF: 0.741 AC: 1567 AN: 2114

Alfa AF: 0.639 Hom.: 2957

Bravo AF: 0.732

Asia WGS AF: 0.834 AC: 2895 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1152746; hg19: chr1-192796905;