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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.288-4675C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.165-4675C>T		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.340-4675C>T		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.565-4675C>T		intron_variant	Intron 4 of 5

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 v4.3

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;