rs9427560

Variant names:

• chr1-192581536-A-G
• rs9427560
• ENST00000434300.3:n.164+12063T>C

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.164+12063T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,038 control chromosomes in the GnomAD database, including 2,876 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 0.15 (2876 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.287+12063T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.164+12063T>C		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.339+12063T>C		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.564+12063T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23139 AN: 151920 Hom.: 2871 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0451

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.152 AC: 23169 AN: 152038 Hom.: 2876 Cov.: 32 AF XY: 0.149 AC XY: 11084 AN XY: 74334

African (AFR) AF: 0.344 AC: 14252 AN: 41438

American (AMR) AF: 0.0863 AC: 1317 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0451 AC: 156 AN: 3462

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0751 AC: 362 AN: 4818

European-Finnish (FIN) AF: 0.0931 AC: 986 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5776 AN: 67966

Other (OTH) AF: 0.111 AC: 235 AN: 2114

Alfa AF: 0.126 Hom.: 330

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.19
DANN	Benign	0.30
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9427560; hg19: chr1-192550666;