rs842796

Variant names:

• chr1-192933285-T-C
• rs842796
• ENST00000646606.1:n.295+14028A>G

Variant summary

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

The ENST00000646606.1(ENSG00000285280):​n.295+14028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,990 control chromosomes in the GnomAD database, including 29,055 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 0.62 (29055 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000646606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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	ENST00000646606.1	n.295+14028A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93538 AN: 151872 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.616 AC: 93635 AN: 151990 Hom.: 29055 Cov.: 32 AF XY: 0.614 AC XY: 45567 AN XY: 74256

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.586

Alfa AF: 0.606 Hom.: 56678

Bravo AF: 0.619

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs842796; hg19: chr1-192902415; COSMIC: COSV71625402;