20-44354947-C-T

Position:

• chr20-44354947-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.224+72G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,234 control chromosomes in the GnomAD database, including 946 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 0.10 (946 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: R3HDML-AS1 NR_184036.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
R3HDML-AS1	NR_184036.1	n.224+72G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
R3HDML-AS1	ENST00000438702.1	n.167+72G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 15186 AN: 152068 Hom.: 948 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.146 AC: 7 AN: 48 Hom.: 0 AF XY: 0.143 AC XY: 4 AN XY: 28

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0998 AC: 15183 AN: 152186 Hom.: 946 Cov.: 32 AF XY: 0.0971 AC XY: 7223 AN XY: 74414

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0854 Hom.: 142

Bravo AF: 0.0979

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11508796; hg19: chr20-42983587;