20-44354947-C-T

Variant names:

• chr20-44354947-C-T
• rs11508796
• ENST00000438702.1:n.167+72G>A

Variant summary

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

The ENST00000438702.1(R3HDML-AS1):​n.167+72G>A variant causes a intron 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 ENST00000438702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438702.1. 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.224+72G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	R3HDML-AS1	ENST00000438702.1	TSL:5	n.167+72G>A		intron	N/A
	R3HDML-AS1	ENST00000735551.1		n.280+72G>A		intron	N/A

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.133 AC: 4 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0478 AC: 1986 AN: 41540

American (AMR) AF: 0.0907 AC: 1385 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0709 AC: 342 AN: 4826

European-Finnish (FIN) AF: 0.0985 AC: 1043 AN: 10588

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9395 AN: 68002

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0850 Hom.: 143

Bravo AF: 0.0979

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.45
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs11508796; hg19: chr20-42983587;