rs10494665

Variant names:

• chr1-192475126-G-A
• rs10494665
• ENST00000642855.1:n.859+913C>T

Variant summary

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

The ENST00000642855.1(ENSG00000285280):​n.859+913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,194 control chromosomes in the GnomAD database, including 182 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 0.047 (182 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0867 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	ENST00000642855.1	n.859+913C>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7083 AN: 152076 Hom.: 179 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0466 AC: 7086 AN: 152194 Hom.: 182 Cov.: 32 AF XY: 0.0478 AC XY: 3557 AN XY: 74406

Gnomad4 AFR AF: 0.0275 AC: 0.0274728 AN: 0.0274728

Gnomad4 AMR AF: 0.0319 AC: 0.031933 AN: 0.031933

Gnomad4 ASJ AF: 0.0427 AC: 0.0426513 AN: 0.0426513

Gnomad4 EAS AF: 0.0936 AC: 0.0935932 AN: 0.0935932

Gnomad4 SAS AF: 0.0685 AC: 0.0684932 AN: 0.0684932

Gnomad4 FIN AF: 0.0889 AC: 0.0889183 AN: 0.0889183

Gnomad4 NFE AF: 0.0491 AC: 0.0491029 AN: 0.0491029

Gnomad4 OTH AF: 0.0403 AC: 0.0402844 AN: 0.0402844

Alfa AF: 0.0479 Hom.: 60

Bravo AF: 0.0412

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494665; hg19: chr1-192444256;