chr1-192572342-C-G

Variant names:

• chr1-192572342-C-G
• rs1359062
• ENST00000434300.3:n.165-5126G>C

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.165-5126G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,108 control chromosomes in the GnomAD database, including 43,504 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 0.75 (43504 hom., cov: 31)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 45 publications found

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.288-5126G>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.165-5126G>C		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.340-5126G>C		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.565-5126G>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113561 AN: 151990 Hom.: 43494 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.747 AC: 113603 AN: 152108 Hom.: 43504 Cov.: 31 AF XY: 0.753 AC XY: 56009 AN XY: 74354

African (AFR) AF: 0.564 AC: 23387 AN: 41444

American (AMR) AF: 0.760 AC: 11604 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2907 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4100 AN: 5176

South Asian (SAS) AF: 0.910 AC: 4390 AN: 4822

European-Finnish (FIN) AF: 0.868 AC: 9214 AN: 10610

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55412 AN: 67992

Other (OTH) AF: 0.752 AC: 1589 AN: 2112

Alfa AF: 0.730 Hom.: 2370

Bravo AF: 0.730

Asia WGS AF: 0.846 AC: 2943 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs1359062; hg19: chr1-192541472;