chr20-44353707-C-T

Variant names:

• chr20-44353707-C-T
• rs6031544
• ENST00000438702.1:n.167+1312G>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+1312G>A variant causes a intron 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 ENST00000438702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 12 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=-0.98).
• 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 rank	MANE	Protein	UniProt
R3HDML-AS1	NR_184036.1	n.224+1312G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
R3HDML-AS1	ENST00000438702.1	n.167+1312G>A		intron_variant	Intron 1 of 3	5
R3HDML-AS1	ENST00000735551.1	n.280+1312G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.275 AC: 11392 AN: 41420

American (AMR) AF: 0.474 AC: 7229 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2268 AN: 5150

South Asian (SAS) AF: 0.374 AC: 1804 AN: 4818

European-Finnish (FIN) AF: 0.311 AC: 3268 AN: 10524

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20897 AN: 67948

Other (OTH) AF: 0.331 AC: 697 AN: 2104

Alfa AF: 0.323 Hom.: 27102

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6031544; hg19: chr20-42982347;