chr20-58589799-A-G

Variant names:

• chr20-58589799-A-G
• rs127430
• ENST00000427140.5:n.944-28941A>G

Variant summary

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

The ENST00000427140.5(APCDD1L-DT):​n.944-28941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,202 control chromosomes in the GnomAD database, including 47,624 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 0.78 (47624 hom., cov: 33)
• Consequence: APCDD1L-DT ENST00000427140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 13 publications found

Genes affected

APCDD1L-DT (HGNC:27152): (APCDD1L divergent transcript)

ENSG00000295904 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APCDD1L-DT	NR_034147.1	n.944-28941A>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APCDD1L-DT	ENST00000427140.5	n.944-28941A>G		intron_variant	Intron 6 of 6	2
APCDD1L-DT	ENST00000445984.6	n.571-16952A>G		intron_variant	Intron 4 of 4	3
APCDD1L-DT	ENST00000701694.1	n.566-16952A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119375 AN: 152084 Hom.: 47594 Cov.: 33

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.785 AC: 119462 AN: 152202 Hom.: 47624 Cov.: 33 AF XY: 0.784 AC XY: 58365 AN XY: 74398

African (AFR) AF: 0.641 AC: 26597 AN: 41512

American (AMR) AF: 0.835 AC: 12786 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2736 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3449 AN: 5144

South Asian (SAS) AF: 0.743 AC: 3590 AN: 4832

European-Finnish (FIN) AF: 0.891 AC: 9451 AN: 10606

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58135 AN: 68008

Other (OTH) AF: 0.801 AC: 1693 AN: 2114

Alfa AF: 0.839 Hom.: 92257

Bravo AF: 0.777

Asia WGS AF: 0.725 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs127430; hg19: chr20-57164855;