ENST00000653439.2:n.340-3199C>T

Variant names:

• chr15-33298416-G-A
• rs8031347
• ENST00000653439.2:n.340-3199C>T

Variant summary

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

The ENST00000653439.2(RYR3-DT):​n.340-3199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,124 control chromosomes in the GnomAD database, including 6,121 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 0.28 (6121 hom., cov: 33)
• Consequence: RYR3-DT ENST00000653439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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.340-3199C>T		intron	N/A
	RYR3-DT	ENST00000666561.1		n.316-3199C>T		intron	N/A
	ENSG00000293377	ENST00000806662.1		n.438+11734C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42144 AN: 152006 Hom.: 6118 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.277 AC: 42156 AN: 152124 Hom.: 6121 Cov.: 33 AF XY: 0.278 AC XY: 20704 AN XY: 74350

African (AFR) AF: 0.320 AC: 13280 AN: 41474

American (AMR) AF: 0.225 AC: 3435 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1641 AN: 5178

South Asian (SAS) AF: 0.338 AC: 1628 AN: 4812

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10574

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17352 AN: 68012

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.264 Hom.: 21428

Bravo AF: 0.275

Asia WGS AF: 0.344 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.56
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs8031347; hg19: chr15-33590617;