ENST00000644058.2:n.202-42483C>G

Variant names:

• chr1-192808677-G-C
• rs2746072
• ENST00000644058.2:n.202-42483C>G

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-42483C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,020 control chromosomes in the GnomAD database, including 6,588 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 0.29 (6588 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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.202-42483C>G		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-42483C>G		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-16209C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44234 AN: 151902 Hom.: 6588 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.291 AC: 44250 AN: 152020 Hom.: 6588 Cov.: 32 AF XY: 0.291 AC XY: 21606 AN XY: 74292

African (AFR) AF: 0.310 AC: 12844 AN: 41474

American (AMR) AF: 0.257 AC: 3929 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2294 AN: 5146

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4816

European-Finnish (FIN) AF: 0.253 AC: 2683 AN: 10584

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19007 AN: 67924

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.140 Hom.: 253

Bravo AF: 0.291

Asia WGS AF: 0.392 AC: 1357 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.42
PhyloP100		-0.36
PromoterAI		0.031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2746072; hg19: chr1-192777807;