chr1-192244106-G-A

Variant names:

• chr1-192244106-G-A
• rs1175152
• ENST00000643151.1:n.306-4316C>T

Variant summary

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

The ENST00000643151.1(ENSG00000285280):​n.306-4316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,898 control chromosomes in the GnomAD database, including 17,959 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 0.47 (17959 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000643151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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	ENST00000643151.1	n.306-4316C>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71846 AN: 151780 Hom.: 17933 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.473 AC: 71911 AN: 151898 Hom.: 17959 Cov.: 32 AF XY: 0.473 AC XY: 35095 AN XY: 74214

African (AFR) AF: 0.619 AC: 25626 AN: 41426

American (AMR) AF: 0.353 AC: 5384 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3468

East Asian (EAS) AF: 0.186 AC: 966 AN: 5184

South Asian (SAS) AF: 0.453 AC: 2184 AN: 4818

European-Finnish (FIN) AF: 0.516 AC: 5442 AN: 10546

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29481 AN: 67886

Other (OTH) AF: 0.435 AC: 915 AN: 2104

Alfa AF: 0.452 Hom.: 1995

Bravo AF: 0.463

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1175152; hg19: chr1-192213236;