rs2816312

Variant names:

• chr1-192581066-A-G
• rs2816312
• ENST00000434300.3:n.164+12533T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-192581066-A-G
• chr1-192581066-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.164+12533T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,990 control chromosomes in the GnomAD database, including 2,096 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 0.14 (2096 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.287+12533T>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+12533T>C		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.339+12533T>C		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.564+12533T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20605 AN: 151872 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.136 AC: 20633 AN: 151990 Hom.: 2096 Cov.: 32 AF XY: 0.132 AC XY: 9815 AN XY: 74296

African (AFR) AF: 0.289 AC: 11990 AN: 41426

American (AMR) AF: 0.0814 AC: 1243 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0468 AC: 162 AN: 3462

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5164

South Asian (SAS) AF: 0.0752 AC: 362 AN: 4814

European-Finnish (FIN) AF: 0.0807 AC: 854 AN: 10584

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

European-Non Finnish (NFE) AF: 0.0843 AC: 5730 AN: 67960

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0782 Hom.: 175

Bravo AF: 0.143

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.38
DANN	Benign	0.39
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2816312; hg19: chr1-192550196;