19-55054266-G-C

Variant summary

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

The NM_001145971.2(RDH13):c.340+2387C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,184 control chromosomes in the GnomAD database, including 1,861 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 0.15 (1861 hom., cov: 32)
• Consequence: RDH13 NM_001145971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

RDH13 (HGNC:19978): (retinol dehydrogenase 13) This gene encodes a mitochondrial short-chain dehydrogenase/reductase, which catalyzes the reduction and oxidation of retinoids. The encoded enzyme may function in retinoic acid production and may also protect the mitochondria against oxidative stress. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RDH13	NM_001145971.2	c.340+2387C>G		intron_variant		ENST00000415061.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RDH13	ENST00000415061.8	c.340+2387C>G		intron_variant		1	NM_001145971.2	P1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22132 AN: 152066 Hom.: 1858 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.146 AC: 22163 AN: 152184 Hom.: 1861 Cov.: 32 AF XY: 0.146 AC XY: 10840 AN XY: 74408

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0631 Hom.: 77

Bravo AF: 0.151

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.9
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672111; hg19: chr19-55565634; COSMIC: COSV52562906; COSMIC: COSV52562906;