chr1-192400980-T-C

Position:

• chr1-192400980-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642855.1(ENSG00000285280):​n.860-13166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 151,846 control chromosomes in the GnomAD database, including 61,626 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 0.90 (61626 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000642855.1	n.860-13166A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136523 AN: 151728 Hom.: 61602 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.900 AC: 136602 AN: 151846 Hom.: 61626 Cov.: 32 AF XY: 0.897 AC XY: 66572 AN XY: 74214

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.904

Alfa AF: 0.932 Hom.: 86792

Bravo AF: 0.897

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2369810; hg19: chr1-192370110;