20-44355240-T-C

Variant names:

• chr20-44355240-T-C
• rs377144780
• NR_184036.1:n.3A>G

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NR_184036.1(R3HDML-AS1):​n.3A>G 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 0.0008 in 164,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00080 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00079 (0 hom.)
• Consequence: R3HDML-AS1 NR_184036.1 non_coding_transcript_exon
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: 0.0690
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 20-44355240-T-C is Benign according to our data. Variant chr20-44355240-T-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 435430.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_184036.1. 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.3A>G		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDML-AS1	ENST00000735551.1		n.160-101A>G		intron	N/A
	R3HDML-AS1	ENST00000438702.1	TSL:5	n.-55A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.000802 AC: 122 AN: 152154 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.000478

GnomAD4 exome AF: 0.000790 AC: 10 AN: 12660 Hom.: 0 AF XY: 0.00117 AC XY: 8 AN XY: 6822

African (AFR) AF: 0.00 AC: 0 AN: 114

American (AMR) AF: 0.000643 AC: 2 AN: 3110

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 82

East Asian (EAS) AF: 0.00 AC: 0 AN: 736

South Asian (SAS) AF: 0.00 AC: 0 AN: 2194

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 84

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 14

European-Non Finnish (NFE) AF: 0.00138 AC: 8 AN: 5816

Other (OTH) AF: 0.00 AC: 0 AN: 510

GnomAD4 genome AF: 0.000801 AC: 122 AN: 152272 Hom.: 1 Cov.: 32 AF XY: 0.000712 AC XY: 53 AN XY: 74456

African (AFR) AF: 0.000241 AC: 10 AN: 41540

American (AMR) AF: 0.000523 AC: 8 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00141 AC: 96 AN: 68022

Other (OTH) AF: 0.000473 AC: 1 AN: 2114

Alfa AF: 0.000157 Hom.: 0

Bravo AF: 0.000854

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	-	1	Maturity-onset diabetes of the young (1)
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.68
PhyloP100		0.069
PromoterAI		-0.0019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs377144780; hg19: chr20-42983880;