rs2760524

Variant names:

• chr1-192561418-A-G
• rs2760524
• ENST00000434300.3:n.234+5729T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-192561418-A-G
• chr1-192561418-A-T

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.234+5729T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,146 control chromosomes in the GnomAD database, including 56,658 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 0.86 (56658 hom., cov: 31)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 26 publications found

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.357+5729T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.234+5729T>C		intron_variant	Intron 3 of 3	5
ENSG00000285280	ENST00000642855.1	n.409+5729T>C		intron_variant	Intron 4 of 7
ENSG00000285280	ENST00000644058.2	n.634+5729T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130821 AN: 152028 Hom.: 56598 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.861 AC: 130937 AN: 152146 Hom.: 56658 Cov.: 31 AF XY: 0.863 AC XY: 64174 AN XY: 74380

African (AFR) AF: 0.951 AC: 39466 AN: 41498

American (AMR) AF: 0.805 AC: 12306 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4152 AN: 5186

South Asian (SAS) AF: 0.913 AC: 4392 AN: 4812

European-Finnish (FIN) AF: 0.868 AC: 9185 AN: 10580

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55663 AN: 67994

Other (OTH) AF: 0.841 AC: 1777 AN: 2112

Alfa AF: 0.845 Hom.: 9825

Bravo AF: 0.860

Asia WGS AF: 0.872 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.67
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2760524; hg19: chr1-192530548;