1-192915745-C-A

Variant names:

• chr1-192915745-C-A
• rs10494676
• ENST00000644058.2:n.201+9867G>T

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.201+9867G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 151,932 control chromosomes in the GnomAD database, including 1,766 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 0.095 (1766 hom., cov: 33)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644058.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285280	ENST00000644058.2		n.201+9867G>T		intron	N/A
	ENSG00000285280	ENST00000644134.1		n.104+9867G>T		intron	N/A
	ENSG00000285280	ENST00000644436.1		n.105-4264G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0950 AC: 14417 AN: 151814 Hom.: 1761 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.00797

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0951 AC: 14442 AN: 151932 Hom.: 1766 Cov.: 33 AF XY: 0.0929 AC XY: 6896 AN XY: 74266

African (AFR) AF: 0.288 AC: 11932 AN: 41404

American (AMR) AF: 0.0513 AC: 783 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5174

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4816

European-Finnish (FIN) AF: 0.00797 AC: 84 AN: 10540

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1123 AN: 67946

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.00377 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs10494676; hg19: chr1-192884875;