rs10754012

Variant names:

• chr1-192523765-A-G
• rs10754012
• ENST00000434300.3:n.235-5802T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-192523765-A-G
• chr1-192523765-A-T

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.235-5802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,172 control chromosomes in the GnomAD database, including 53,307 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 0.83 (53307 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 12 publications found

Genes affected

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

ENSG00000236069 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.358-5802T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.235-5802T>C		intron_variant	Intron 3 of 3	5
ENSG00000236069	ENST00000642657.1	n.717+5859A>G		intron_variant	Intron 1 of 2
ENSG00000285280	ENST00000642855.1	n.410-31796T>C		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126755 AN: 152054 Hom.: 53248 Cov.: 32

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.834 AC: 126871 AN: 152172 Hom.: 53307 Cov.: 32 AF XY: 0.835 AC XY: 62116 AN XY: 74386

African (AFR) AF: 0.946 AC: 39324 AN: 41554

American (AMR) AF: 0.801 AC: 12224 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4103 AN: 5176

South Asian (SAS) AF: 0.884 AC: 4263 AN: 4822

European-Finnish (FIN) AF: 0.784 AC: 8298 AN: 10588

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53176 AN: 67990

Other (OTH) AF: 0.820 AC: 1731 AN: 2112

Alfa AF: 0.805 Hom.: 17208

Bravo AF: 0.839

Asia WGS AF: 0.846 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.79
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10754012; hg19: chr1-192492895;