rs1671215

chr19-55041651-C-Achr19-55041651-C-Gchr19-55041651-C-T

Variant summary

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

The ENST00000593060.5(GP6-AS1):n.156-1149C>A variant causes a intron, non coding transcript 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: GP6-AS1 ENST00000593060.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GP6-AS1	XR_001754012.3	n.122-1149C>A		intron_variant, non_coding_transcript_variant
RDH13	XM_011526408.4	c.*451G>T		3_prime_UTR_variant	7/7
RDH13	XR_007066569.1	n.1767G>T		non_coding_transcript_exon_variant	8/8
GP6-AS1	XR_001754013.3	n.112-1149C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GP6-AS1	ENST00000593060.5	n.156-1149C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

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

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.645

Alfa AF: 0.664 Hom.: 21753

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1671215; hg19: chr19-55553019;