rs17235910

Variant names:

• chr15-33296299-C-T
• rs17235910
• ENST00000653439.2:n.340-1082G>A

Variant summary

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

The ENST00000653439.2(RYR3-DT):​n.340-1082G>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 ENST00000653439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 2 publications found

Genes affected

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

ENSG00000293377 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653439.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RYR3-DT	ENST00000653439.2		n.340-1082G>A		intron	N/A
	RYR3-DT	ENST00000666561.1		n.316-1082G>A		intron	N/A
	ENSG00000293377	ENST00000806662.1		n.438+13851G>A		intron	N/A

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

African (AFR) AF: 0.0135 AC: 559 AN: 41516

American (AMR) AF: 0.0578 AC: 885 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0439 AC: 152 AN: 3466

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5164

South Asian (SAS) AF: 0.0206 AC: 99 AN: 4814

European-Finnish (FIN) AF: 0.0407 AC: 431 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4407 AN: 67994

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0595 Hom.: 505

Bravo AF: 0.0441

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs17235910; hg19: chr15-33588500;