rs1323292

Variant names:

• chr1-192571891-G-A
• rs1323292
• ENST00000434300.3:n.165-4675C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-192571891-G-A
• chr1-192571891-G-C
• chr1-192571891-G-T

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.165-4675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,198 control chromosomes in the GnomAD database, including 56,498 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 0.86 (56498 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 62 publications found

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434300.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285280	ENST00000434300.3	TSL:5	n.165-4675C>T		intron	N/A
	ENSG00000285280	ENST00000642855.1		n.340-4675C>T		intron	N/A
	ENSG00000285280	ENST00000644058.2		n.565-4675C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130626 AN: 152080 Hom.: 56437 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.859 AC: 130743 AN: 152198 Hom.: 56498 Cov.: 32 AF XY: 0.862 AC XY: 64117 AN XY: 74410

African (AFR) AF: 0.952 AC: 39582 AN: 41572

American (AMR) AF: 0.804 AC: 12281 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2955 AN: 3470

East Asian (EAS) AF: 0.793 AC: 4096 AN: 5168

South Asian (SAS) AF: 0.911 AC: 4387 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9187 AN: 10582

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55481 AN: 67990

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.832 Hom.: 98684

Bravo AF: 0.857

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.46
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1323292; hg19: chr1-192541021;