rs17235910

Positions:

• chr15-33296299-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR3-DT	ENST00000653439.1	n.290-1082G>A		intron_variant, non_coding_transcript_variant
RYR3-DT	ENST00000666561.1	n.316-1082G>A		intron_variant, non_coding_transcript_variant

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;