Variant chr19-10022183-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015725.4(RDH8):c.*434T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 169,150 control chromosomes in the GnomAD database, including 23,015 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 0.52 ( 21099 hom., cov: 31)

Exomes 𝑓: 0.45 ( 1916 hom. )

Consequence

RDH8
NM_015725.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.333

Variant links:

Genes affected

RDH8 (HGNC:14423): (retinol dehydrogenase 8) This gene encodes a member of the short-chain dehydrogenase/reductase family. The encoded protein catalyzes the reduction of all-trans-retinal to all-trans-retinol, the first reaction step of the rhodopsin regeneration pathway. This enzymatic reaction is the rate-limiting step in the visual cycle. [provided by RefSeq, Feb 2014]

RDH8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RDH8	NM_015725.4 link	c.*434T>A		3_prime_UTR_variant	6/6	ENST00000591589.3	NP_056540.3	Q9NYR8K7ELF7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RDH8	ENST00000591589.3 link	c.*434T>A		3_prime_UTR_variant	6/6	1	NM_015725.4	ENSP00000466058.2		Q9NYR8
RDH8	ENST00000651512.1 link	c.*434T>A		3_prime_UTR_variant	6/6			ENSP00000498711.1		K7ELF7

Frequencies

GnomAD3 genomes

AF:

0.521

AC:

79048

AN:

151598

Hom.:

21070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.512

GnomAD4 exome

AF:

0.446

AC:

7773

AN:

17434

Hom.:

1916

Cov.:

AF XY:

0.445

AC XY:

3993

AN XY:

8970

show subpopulations

Gnomad4 AFR exome

AF:

0.589

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.438

Gnomad4 EAS exome

AF:

0.486

Gnomad4 SAS exome

AF:

0.629

Gnomad4 FIN exome

AF:

0.415

Gnomad4 NFE exome

AF:

0.391

Gnomad4 OTH exome

AF:

0.434

GnomAD4 genome

AF:

0.522

AC:

79138

AN:

151716

Hom.:

21099

Cov.:

AF XY:

0.528

AC XY:

39146

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.613

Gnomad4 AMR

AF:

0.545

Gnomad4 ASJ

AF:

0.473

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.678

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.469

Hom.:

2151

Bravo

AF:

0.521

Asia WGS

AF:

0.636

AC:

2213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.5

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over