chr1-192817254-A-C

Variant names:

• chr1-192817254-A-C
• rs10801156
• ENST00000644058.2:n.202-51060T>G

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-51060T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,884 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 1 publications found

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ENSG00000296334 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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.202-51060T>G		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-51060T>G		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.199+9650T>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43040 AN: 151764 Hom.: 6278 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.283 AC: 43048 AN: 151884 Hom.: 6282 Cov.: 32 AF XY: 0.285 AC XY: 21181 AN XY: 74206

African (AFR) AF: 0.268 AC: 11117 AN: 41408

American (AMR) AF: 0.322 AC: 4916 AN: 15254

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

East Asian (EAS) AF: 0.500 AC: 2575 AN: 5150

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4822

European-Finnish (FIN) AF: 0.240 AC: 2530 AN: 10540

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18400 AN: 67926

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.267 Hom.: 810

Bravo AF: 0.288

Asia WGS AF: 0.414 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.33
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10801156; hg19: chr1-192786384;