rs10489516

Variant names:

• chr1-192750241-G-A
• rs10489516
• ENST00000644058.1:n.497+14567C>T

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.497+14567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,114 control chromosomes in the GnomAD database, including 4,124 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 0.16 (4124 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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.497+14567C>T		intron_variant	Intron 3 of 5
ENSG00000285280	ENST00000644134.1	n.408+14567C>T		intron_variant	Intron 3 of 6
ENSG00000285280	ENST00000645822.1	n.673+14567C>T		intron_variant	Intron 5 of 5
ENSG00000285280	ENST00000646999.1	n.564+4680C>T		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24192 AN: 151996 Hom.: 4104 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.159 AC: 24262 AN: 152114 Hom.: 4124 Cov.: 32 AF XY: 0.160 AC XY: 11880 AN XY: 74406

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.0624

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.141

Alfa AF: 0.110 Hom.: 737

Bravo AF: 0.179

Asia WGS AF: 0.132 AC: 455 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489516; hg19: chr1-192719371;