19-55038944-A-G

Variant names:

• chr19-55038944-A-G
• rs1654433
• ENST00000585492.1:n.1001+5961T>C

Variant summary

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

The ENST00000585492.1(ENSG00000267149):​n.1001+5961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,064 control chromosomes in the GnomAD database, including 50,699 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 0.81 (50699 hom., cov: 31)
• Consequence: ENSG00000267149 ENST00000585492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 9 publications found

Genes affected

ENSG00000267149 (HGNC:):

GP6-AS1 (HGNC:55305): (GP6 antisense RNA 1)

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267149	ENST00000585492.1	TSL:2	n.1001+5961T>C		intron	N/A
	GP6-AS1	ENST00000586845.1	TSL:3	n.134-3888A>G		intron	N/A
	GP6-AS1	ENST00000586961.1	TSL:5	n.45-3888A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123612 AN: 151946 Hom.: 50673 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.813 AC: 123695 AN: 152064 Hom.: 50699 Cov.: 31 AF XY: 0.819 AC XY: 60852 AN XY: 74336

African (AFR) AF: 0.715 AC: 29636 AN: 41444

American (AMR) AF: 0.854 AC: 13012 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2677 AN: 3468

East Asian (EAS) AF: 0.976 AC: 5046 AN: 5172

South Asian (SAS) AF: 0.805 AC: 3875 AN: 4816

European-Finnish (FIN) AF: 0.891 AC: 9460 AN: 10612

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57298 AN: 67994

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.824 Hom.: 75137

Bravo AF: 0.805

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1654433; hg19: chr19-55550312;