rs1884614

chr20-44351879-C-T

Variant summary

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

The NR_184036.1(R3HDML-AS1):n.296G>A 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 0.191 in 152,114 control chromosomes in the GnomAD database, including 3,531 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 (3519 hom., cov: 29)
  • Exomes 𝑓: 0.16 (12 hom.)
• Consequence: R3HDML-AS1 NR_184036.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
R3HDML-AS1	NR_184036.1	n.296G>A		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
R3HDML-AS1	ENST00000438702.1	n.239G>A		non_coding_transcript_exon_variant	2/4	5
R3HDML-AS1	ENST00000430481.2	n.224G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28874 AN: 151570 Hom.: 3502 Cov.: 29

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.160 AC: 68 AN: 424 Hom.: 12 Cov.: 0 AF XY: 0.155 AC XY: 39 AN XY: 252

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.458

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.191 AC: 28919 AN: 151690 Hom.: 3519 Cov.: 29 AF XY: 0.199 AC XY: 14776 AN XY: 74076

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.211

Alfa AF: 0.197 Hom.: 841

Bravo AF: 0.202

Asia WGS AF: 0.367 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884614; hg19: chr20-42980519;