rs10494677

Positions:

• chr1-192915006-G-A

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.193+10606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 152,070 control chromosomes in the GnomAD database, including 1,763 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 (1763 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000644058.1	n.193+10606C>T		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.104+10606C>T		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000644436.1	n.105-3525C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0949 AC: 14420 AN: 151952 Hom.: 1758 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.00805

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0741

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

GnomAD4 genome AF: 0.0950 AC: 14445 AN: 152070 Hom.: 1763 Cov.: 32 AF XY: 0.0928 AC XY: 6896 AN XY: 74340

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.0517

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.00805

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0458 Hom.: 130

Bravo AF: 0.106

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494677; hg19: chr1-192884136;