rs1671215

Variant names:

• chr19-55041651-C-A
• rs1671215
• ENST00000586331.1:n.239G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-55041651-C-A
• chr19-55041651-C-G
• chr19-55041651-C-T

Variant summary

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

The ENST00000586331.1(RDH13):​n.239G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,116 control chromosomes in the GnomAD database, including 33,131 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 0.66 (33123 hom., cov: 33)
  • Exomes 𝑓: 0.86 (8 hom.)
• Consequence: RDH13 ENST00000586331.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 15 publications found

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]

ENSG00000267149 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDH13	XR_007066569.1	n.1767G>T		non_coding_transcript_exon_variant	Exon 8 of 8
RDH13	XM_011526408.4	c.*451G>T		3_prime_UTR_variant	Exon 7 of 7		XP_011524710.1
GP6-AS1	XR_001754012.3	n.122-1149C>A		intron_variant	Intron 2 of 2
GP6-AS1	XR_001754013.3	n.112-1149C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RDH13	ENST00000586331.1	n.239G>T		non_coding_transcript_exon_variant	Exon 1 of 3	5
RDH13	ENST00000591960.1	n.*444G>T		non_coding_transcript_exon_variant	Exon 3 of 4	5		ENSP00000468422.1
RDH13	ENST00000592423.1	n.1457G>T		non_coding_transcript_exon_variant	Exon 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99771 AN: 151976 Hom.: 33107 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 0.864 AC: 19 AN: 22 Hom.: 8 Cov.: 0 AF XY: 0.938 AC XY: 15 AN XY: 16

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.875 AC: 7 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 8 AN: 8

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.656 AC: 99840 AN: 152094 Hom.: 33123 Cov.: 33 AF XY: 0.658 AC XY: 48915 AN XY: 74352

African (AFR) AF: 0.592 AC: 24568 AN: 41494

American (AMR) AF: 0.605 AC: 9240 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1918 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4235 AN: 5168

South Asian (SAS) AF: 0.628 AC: 3025 AN: 4818

European-Finnish (FIN) AF: 0.739 AC: 7811 AN: 10574

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46959 AN: 67980

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.673 Hom.: 77112

Bravo AF: 0.641

Asia WGS AF: 0.686 AC: 2389 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	0.41
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1671215; hg19: chr19-55553019;