rs2186024

Variant names:

• chr1-192460955-A-C
• rs2186024
• ENST00000642855.1:n.859+15084T>G

Variant summary

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

The ENST00000642855.1(ENSG00000285280):​n.859+15084T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,988 control chromosomes in the GnomAD database, including 17,646 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 0.48 (17646 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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+15084T>G		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72562 AN: 151870 Hom.: 17606 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.478 AC: 72659 AN: 151988 Hom.: 17646 Cov.: 32 AF XY: 0.475 AC XY: 35269 AN XY: 74290

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.464

Alfa AF: 0.451 Hom.: 34028

Bravo AF: 0.492

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186024; hg19: chr1-192430085;