rs6026398

Variant names:

• chr20-58604953-A-G
• rs6026398
• ENST00000427140.5:n.944-13787A>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.944-13787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,044 control chromosomes in the GnomAD database, including 20,639 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 0.48 (20639 hom., cov: 32)
• Consequence: APCDD1L-DT ENST00000427140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99
• Publications: 4 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427140.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APCDD1L-DT	NR_034147.1		n.944-13787A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APCDD1L-DT	ENST00000427140.5	TSL:2	n.944-13787A>G		intron	N/A
	APCDD1L-DT	ENST00000445984.6	TSL:3	n.571-1798A>G		intron	N/A
	APCDD1L-DT	ENST00000701694.1		n.566-1798A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72797 AN: 151926 Hom.: 20591 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.479 AC: 72892 AN: 152044 Hom.: 20639 Cov.: 32 AF XY: 0.472 AC XY: 35092 AN XY: 74328

African (AFR) AF: 0.799 AC: 33153 AN: 41468

American (AMR) AF: 0.414 AC: 6327 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1397 AN: 5158

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2828 AN: 10582

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24285 AN: 67944

Other (OTH) AF: 0.472 AC: 997 AN: 2112

Alfa AF: 0.397 Hom.: 17055

Bravo AF: 0.503

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0040
DANN	Benign	0.29
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs6026398; hg19: chr20-57180009; COSMIC: COSV68574385;