rs16829458

Variant names:

• chr1-192799194-G-A
• rs16829458
• ENST00000644058.1:n.194-33000C>T

Variant summary

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

The ENST00000644058.1(ENSG00000285280):​n.194-33000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 152,106 control chromosomes in the GnomAD database, including 600 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 0.083 (600 hom., cov: 31)
• Consequence: ENSG00000285280 ENST00000644058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 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.194-33000C>T		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-33000C>T		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-6726C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12569 AN: 151988 Hom.: 596 Cov.: 31

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0754

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0828 AC: 12591 AN: 152106 Hom.: 600 Cov.: 31 AF XY: 0.0854 AC XY: 6351 AN XY: 74360

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0754

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0859 Hom.: 371

Bravo AF: 0.0820

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16829458; hg19: chr1-192768324;