1-192801932-C-T

Variant names:

• chr1-192801932-C-T
• rs2179653
• ENST00000644058.2:n.202-35738G>A

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-35738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,128 control chromosomes in the GnomAD database, including 1,401 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 (1401 hom., cov: 33)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• 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=-0.99).
• 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	ENST00000644058.2	n.202-35738G>A		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-35738G>A		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-9464G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18203 AN: 152010 Hom.: 1400 Cov.: 33

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.120 AC: 18200 AN: 152128 Hom.: 1401 Cov.: 33 AF XY: 0.114 AC XY: 8513 AN XY: 74378

African (AFR) AF: 0.0386 AC: 1601 AN: 41512

American (AMR) AF: 0.124 AC: 1901 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3470

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5186

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4824

European-Finnish (FIN) AF: 0.0937 AC: 992 AN: 10582

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

European-Non Finnish (NFE) AF: 0.176 AC: 11939 AN: 67968

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.137 Hom.: 204

Bravo AF: 0.120

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.040
DANN	Benign	0.67
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2179653; hg19: chr1-192771062;