ENST00000518355.3:n.342-367C>T

Variant names:

• chr8-73361956-C-T
• rs12679254
• ENST00000518355.3:n.342-367C>T

Variant summary

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

The ENST00000518355.3(ENSG00000253339):​n.342-367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,012 control chromosomes in the GnomAD database, including 7,072 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 0.27 (7072 hom., cov: 31)
• Consequence: ENSG00000253339 ENST00000518355.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 9 publications found

Genes affected

ENSG00000253339 (HGNC:):

RDH10-AS1 (HGNC:51658): (RDH10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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
ENSG00000253339	ENST00000518355.3	n.342-367C>T		intron_variant	Intron 1 of 1	4
ENSG00000253339	ENST00000519134.1	n.316-367C>T		intron_variant	Intron 1 of 1	4
RDH10-AS1	ENST00000661600.1	n.413+7257G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41505 AN: 151894 Hom.: 7061 Cov.: 31

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.273 AC: 41537 AN: 152012 Hom.: 7072 Cov.: 31 AF XY: 0.280 AC XY: 20803 AN XY: 74284

African (AFR) AF: 0.0788 AC: 3271 AN: 41488

American (AMR) AF: 0.401 AC: 6112 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2678 AN: 5156

South Asian (SAS) AF: 0.428 AC: 2062 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3291 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21778 AN: 67952

Other (OTH) AF: 0.299 AC: 631 AN: 2110

Alfa AF: 0.308 Hom.: 19484

Bravo AF: 0.270

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.1
DANN	Benign	0.90
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12679254; hg19: chr8-74274191;