rs2676071

Variant names:

• chr15-33304875-C-A
• rs2676071
• ENST00000559457.2:n.220-937G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-33304875-C-A
• chr15-33304875-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000559457.2(RYR3-DT):​n.220-937G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RYR3-DT ENST00000559457.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 7 publications found

Genes affected

RYR3-DT (HGNC:51417): (RYR3 divergent transcript)

ENSG00000293377 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR3-DT	NR_120326.1	n.197-937G>T		intron_variant	Intron 2 of 2
RYR3-DT	NR_120327.1	n.183-937G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR3-DT	ENST00000559457.2	n.220-937G>T		intron_variant	Intron 2 of 2	3
RYR3-DT	ENST00000561458.6	n.507-937G>T		intron_variant	Intron 2 of 2	2
RYR3-DT	ENST00000653439.2	n.339+5275G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2676071; hg19: chr15-33597076;