chr1-192801422-G-T

Variant names:

• chr1-192801422-G-T
• rs1342809
• ENST00000644058.2:n.202-35228C>A

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-35228C>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 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644058.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285280	ENST00000644058.2		n.202-35228C>A		intron	N/A
	ENSG00000285280	ENST00000644134.1		n.105-35228C>A		intron	N/A
	ENSG00000285280	ENST00000645822.1		n.200-8954C>A		intron	N/A

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

African (AFR) AF: 0.0322 AC: 1335 AN: 41518

American (AMR) AF: 0.124 AC: 1892 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.0513 AC: 266 AN: 5184

South Asian (SAS) AF: 0.0610 AC: 294 AN: 4822

European-Finnish (FIN) AF: 0.0940 AC: 995 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11921 AN: 67962

Other (OTH) AF: 0.139 AC: 294 AN: 2108

Alfa AF: 0.103 Hom.: 449

Bravo AF: 0.118

Asia WGS AF: 0.0650 AC: 229 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1342809; hg19: chr1-192770552;