20-44351775-C-G

Variant names:

• chr20-44351775-C-G
• rs1884613
• ENST00000430481.2:n.235+93G>C

Variant summary

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

The ENST00000430481.2(R3HDML-AS1):​n.235+93G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 150,376 control chromosomes in the GnomAD database, including 3,473 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 0.19 (3473 hom., cov: 29)
  • Exomes 𝑓: 0.18 (24 hom.)
  • Failed GnomAD Quality Control
• Consequence: R3HDML-AS1 ENST00000430481.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

R3HDML-AS1 (HGNC:55830): (R3HDML antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
R3HDML-AS1	NR_184036.1	n.307+93G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
R3HDML-AS1	ENST00000430481.2	n.235+93G>C		intron_variant	Intron 1 of 1	2
R3HDML-AS1	ENST00000438702.1	n.250+93G>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28263 AN: 150230 Hom.: 3456 Cov.: 29

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.209

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.181 AC: 121 AN: 670 Hom.: 24 AF XY: 0.183 AC XY: 89 AN XY: 486

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.667

Gnomad4 EAS exome AF: 0.400

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.188 AC: 28304 AN: 150376 Hom.: 3473 Cov.: 29 AF XY: 0.197 AC XY: 14434 AN XY: 73368

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.209

Alfa AF: 0.0882 Hom.: 132

Bravo AF: 0.198

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884613; hg19: chr20-42980415;