rs1933695

Variant names:

• chr1-192795690-G-A
• rs1933695
• ENST00000644058.2:n.202-29496C>T

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-29496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,990 control chromosomes in the GnomAD database, including 1,400 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 (1400 hom., cov: 31)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 6 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=-0.91).
• 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.202-29496C>T		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-29496C>T		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-3222C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18159 AN: 151872 Hom.: 1399 Cov.: 31

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.119 AC: 18156 AN: 151990 Hom.: 1400 Cov.: 31 AF XY: 0.114 AC XY: 8499 AN XY: 74278

African (AFR) AF: 0.0385 AC: 1597 AN: 41458

American (AMR) AF: 0.124 AC: 1895 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3468

East Asian (EAS) AF: 0.0473 AC: 244 AN: 5160

South Asian (SAS) AF: 0.0624 AC: 301 AN: 4826

European-Finnish (FIN) AF: 0.0938 AC: 990 AN: 10550

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

European-Non Finnish (NFE) AF: 0.176 AC: 11929 AN: 67968

Other (OTH) AF: 0.142 AC: 299 AN: 2108

Alfa AF: 0.161 Hom.: 3703

Bravo AF: 0.120

Asia WGS AF: 0.0660 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1933695; hg19: chr1-192764820;