20-58618493-T-C

Variant names:

• chr20-58618493-T-C
• rs6128386
• ENST00000427140.5:n.944-247T>C

Variant summary

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

The ENST00000427140.5(APCDD1L-DT):​n.944-247T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,970 control chromosomes in the GnomAD database, including 16,708 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 0.43 (16708 hom., cov: 32)
• Consequence: APCDD1L-DT ENST00000427140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 9 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APCDD1L-DT	NR_034147.1	n.944-247T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APCDD1L-DT	ENST00000427140.5	n.944-247T>C		intron_variant	Intron 6 of 6	2
APCDD1L-DT	ENST00000733472.1	n.571-4317T>C		intron_variant	Intron 4 of 4
APCDD1L-DT	ENST00000733473.1	n.566-247T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65200 AN: 151852 Hom.: 16681 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.429 AC: 65269 AN: 151970 Hom.: 16708 Cov.: 32 AF XY: 0.428 AC XY: 31762 AN XY: 74272

African (AFR) AF: 0.721 AC: 29898 AN: 41450

American (AMR) AF: 0.365 AC: 5576 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1481 AN: 3464

East Asian (EAS) AF: 0.469 AC: 2413 AN: 5146

South Asian (SAS) AF: 0.406 AC: 1953 AN: 4812

European-Finnish (FIN) AF: 0.269 AC: 2850 AN: 10580

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19822 AN: 67940

Other (OTH) AF: 0.436 AC: 920 AN: 2108

Alfa AF: 0.335 Hom.: 37497

Bravo AF: 0.447

Asia WGS AF: 0.478 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.66
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6128386; hg19: chr20-57193549;