chr1-192801803-A-G

Variant names:

• chr1-192801803-A-G
• rs1890397
• ENST00000644058.2:n.202-35609T>C

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-35609T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,930 control chromosomes in the GnomAD database, including 22,032 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 0.54 (22032 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285280	ENST00000644058.2		n.202-35609T>C		intron	N/A
	ENSG00000285280	ENST00000644134.1		n.105-35609T>C		intron	N/A
	ENSG00000285280	ENST00000645822.1		n.200-9335T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81564 AN: 151812 Hom.: 22022 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.537 AC: 81608 AN: 151930 Hom.: 22032 Cov.: 32 AF XY: 0.534 AC XY: 39645 AN XY: 74244

African (AFR) AF: 0.566 AC: 23439 AN: 41400

American (AMR) AF: 0.516 AC: 7883 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3150 AN: 5170

South Asian (SAS) AF: 0.571 AC: 2751 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4338 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36087 AN: 67948

Other (OTH) AF: 0.540 AC: 1142 AN: 2114

Alfa AF: 0.536 Hom.: 37031

Bravo AF: 0.543

Asia WGS AF: 0.620 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.82
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1890397; hg19: chr1-192770933;