rs17235910

Variant names:

• chr15-33296299-C-T
• rs17235910
• ENST00000653439.1:n.290-1082G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653439.1(RYR3-DT):​n.290-1082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 152,166 control chromosomes in the GnomAD database, including 213 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 0.045 (213 hom., cov: 32)
• Consequence: RYR3-DT ENST00000653439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR3-DT	ENST00000653439.1	n.290-1082G>A		intron_variant	Intron 1 of 1
RYR3-DT	ENST00000666561.1	n.316-1082G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6805 AN: 152048 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0439

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0208

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0447 AC: 6804 AN: 152166 Hom.: 213 Cov.: 32 AF XY: 0.0438 AC XY: 3260 AN XY: 74394

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0439

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0611 Hom.: 424

Bravo AF: 0.0441

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17235910; hg19: chr15-33588500;