rs6031544

chr20-44353707-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+1312G>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 0.325 in 151,882 control chromosomes in the GnomAD database, including 8,490 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 0.33 (8490 hom., cov: 32)
• Consequence: R3HDML-AS1 NR_184036.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
R3HDML-AS1	NR_184036.1	n.224+1312G>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+1312G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49327 AN: 151762 Hom.: 8472 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.332

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.325 AC: 49380 AN: 151882 Hom.: 8490 Cov.: 32 AF XY: 0.329 AC XY: 24444 AN XY: 74204

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.331

Alfa AF: 0.322 Hom.: 16528

Bravo AF: 0.339

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6031544; hg19: chr20-42982347;