ENST00000644058.2:n.202-28624C>T

Variant names:

• chr1-192794818-G-A
• rs10801153
• ENST00000644058.2:n.202-28624C>T

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-28624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,056 control chromosomes in the GnomAD database, including 5,764 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 0.27 (5764 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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.202-28624C>T		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-28624C>T		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-2350C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41264 AN: 151936 Hom.: 5763 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.271 AC: 41265 AN: 152056 Hom.: 5764 Cov.: 32 AF XY: 0.271 AC XY: 20165 AN XY: 74330

African (AFR) AF: 0.229 AC: 9493 AN: 41484

American (AMR) AF: 0.251 AC: 3834 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2329 AN: 5172

South Asian (SAS) AF: 0.292 AC: 1409 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2815 AN: 10546

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19253 AN: 67962

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.281 Hom.: 18414

Bravo AF: 0.267

Asia WGS AF: 0.393 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10801153; hg19: chr1-192763948;