ENST00000430481.3:n.228G>A

Variant names:

• chr20-44351879-C-T
• rs1884614
• ENST00000430481.3:n.228G>A

Variant summary

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

The ENST00000430481.3(R3HDML-AS1):​n.228G>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 ENST00000430481.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 38 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430481.3. 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
	R3HDML-AS1	NR_184036.1		n.296G>A		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDML-AS1	ENST00000430481.3	TSL:2	n.228G>A		non_coding_transcript_exon	Exon 1 of 3
	R3HDML-AS1	ENST00000438702.1	TSL:5	n.239G>A		non_coding_transcript_exon	Exon 2 of 4
	R3HDML-AS1	ENST00000735551.1		n.352G>A		non_coding_transcript_exon	Exon 3 of 5

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

African (AFR) AF: 0.0714 AC: 1 AN: 14

American (AMR) AF: 0.400 AC: 4 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 2 AN: 12

East Asian (EAS) AF: 0.458 AC: 11 AN: 24

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.235 AC: 8 AN: 34

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.124 AC: 39 AN: 314

Other (OTH) AF: 0.300 AC: 3 AN: 10

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

African (AFR) AF: 0.108 AC: 4472 AN: 41362

American (AMR) AF: 0.375 AC: 5709 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3466

East Asian (EAS) AF: 0.441 AC: 2250 AN: 5106

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2221 AN: 10504

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11349 AN: 67916

Other (OTH) AF: 0.211 AC: 445 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs1884614; hg19: chr20-42980519;