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
• Publications: 3 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=-0.88).
• 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

African (AFR) AF: 0.0275 AC: 1141 AN: 41532

American (AMR) AF: 0.0319 AC: 488 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.0936 AC: 485 AN: 5182

South Asian (SAS) AF: 0.0685 AC: 330 AN: 4818

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10594

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3339 AN: 68000

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10494665; hg19: chr1-192444256;