20-44351775-C-G

Variant names:

• chr20-44351775-C-G
• rs1884613
• ENST00000430481.3:n.239+93G>C

Variant summary

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

The ENST00000430481.3(R3HDML-AS1):​n.239+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 ENST00000430481.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 46 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDML-AS1	NR_184036.1		n.307+93G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDML-AS1	ENST00000430481.3	TSL:2	n.239+93G>C		intron	N/A
	R3HDML-AS1	ENST00000438702.1	TSL:5	n.250+93G>C		intron	N/A
	R3HDML-AS1	ENST00000735551.1		n.363+93G>C		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 18

American (AMR) AF: 0.667 AC: 8 AN: 12

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.400 AC: 16 AN: 40

South Asian (SAS) AF: 0.100 AC: 2 AN: 20

European-Finnish (FIN) AF: 0.263 AC: 10 AN: 38

Middle Eastern (MID) AF: 0.125 AC: 1 AN: 8

European-Non Finnish (NFE) AF: 0.160 AC: 80 AN: 500

Other (OTH) AF: 0.118 AC: 4 AN: 34

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

African (AFR) AF: 0.0976 AC: 3995 AN: 40948

American (AMR) AF: 0.376 AC: 5669 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3462

East Asian (EAS) AF: 0.448 AC: 2248 AN: 5020

South Asian (SAS) AF: 0.310 AC: 1427 AN: 4598

European-Finnish (FIN) AF: 0.211 AC: 2190 AN: 10370

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

European-Non Finnish (NFE) AF: 0.168 AC: 11329 AN: 67596

Other (OTH) AF: 0.209 AC: 438 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.46
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1884613; hg19: chr20-42980415;