1-192523765-A-G

Variant names:

• chr1-192523765-A-G
• rs10754012
• ENST00000434300.3:n.235-5802T>C

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.235-5802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,172 control chromosomes in the GnomAD database, including 53,307 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 0.83 (53307 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 12 publications found

Genes affected

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

ENSG00000236069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434300.3. 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	ENST00000434300.3	TSL:5	n.235-5802T>C		intron	N/A
	ENSG00000236069	ENST00000642657.1		n.717+5859A>G		intron	N/A
	ENSG00000285280	ENST00000642855.1		n.410-31796T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126755 AN: 152054 Hom.: 53248 Cov.: 32

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.834 AC: 126871 AN: 152172 Hom.: 53307 Cov.: 32 AF XY: 0.835 AC XY: 62116 AN XY: 74386

African (AFR) AF: 0.946 AC: 39324 AN: 41554

American (AMR) AF: 0.801 AC: 12224 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4103 AN: 5176

South Asian (SAS) AF: 0.884 AC: 4263 AN: 4822

European-Finnish (FIN) AF: 0.784 AC: 8298 AN: 10588

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53176 AN: 67990

Other (OTH) AF: 0.820 AC: 1731 AN: 2112

Alfa AF: 0.805 Hom.: 17208

Bravo AF: 0.839

Asia WGS AF: 0.846 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.79
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10754012; hg19: chr1-192492895;