chr1-192962573-C-T

Variant names:

• chr1-192962573-C-T
• rs7415619
• ENST00000818440.1:n.230-5151G>A

Variant summary

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

The ENST00000818440.1(ENSG00000285280):​n.230-5151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,106 control chromosomes in the GnomAD database, including 453 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 0.070 (453 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000818440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

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

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 (NFE) allele frequency at 95% confidence interval = 0.0932 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	ENST00000818440.1	n.230-5151G>A		intron_variant	Intron 1 of 2
ENSG00000285280	ENST00000818441.1	n.239-5151G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 10601 AN: 151988 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0697 AC: 10608 AN: 152106 Hom.: 453 Cov.: 32 AF XY: 0.0689 AC XY: 5128 AN XY: 74376

African (AFR) AF: 0.0312 AC: 1294 AN: 41492

American (AMR) AF: 0.0803 AC: 1227 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4822

European-Finnish (FIN) AF: 0.0747 AC: 790 AN: 10578

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0952 AC: 6469 AN: 67972

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0827 Hom.: 298

Bravo AF: 0.0708

Asia WGS AF: 0.0170 AC: 60 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	0.32
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7415619; hg19: chr1-192931703;