Variant 18-10455136-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153000.5(APCDD1):c.58+97C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 1,518,442 control chromosomes in the GnomAD database, including 223,069 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26987 hom., cov: 33)

Exomes 𝑓: 0.53 ( 196082 hom. )

Consequence

APCDD1
NM_153000.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.658

Variant links:

Genes affected

APCDD1 (HGNC:15718): (APC down-regulated 1) This locus encodes an inhibitor of the Wnt signaling pathway. Mutations at this locus have been associated with hereditary hypotrichosis simplex. Increased expression of this gene may also be associated with colorectal carcinogenesis.[provided by RefSeq, Sep 2010]

APCDD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 18-10455136-C-T is Benign according to our data. Variant chr18-10455136-C-T is described in ClinVar as [Benign]. Clinvar id is 1221986.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APCDD1	NM_153000.5 linkuse as main transcript	c.58+97C>T		intron_variant		ENST00000355285.10	NP_694545.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
APCDD1	ENST00000355285.10 linkuse as main transcript	c.58+97C>T	intron_variant	1	NM_153000.5	ENSP00000347433	P1
APCDD1	ENST00000578882.1 linkuse as main transcript	c.58+97C>T	intron_variant	3		ENSP00000463104
APCDD1	ENST00000423585.2 linkuse as main transcript	c.58+97C>T	intron_variant, NMD_transcript_variant	3		ENSP00000404930
APCDD1	ENST00000582723.1 linkuse as main transcript	c.58+97C>T	intron_variant, NMD_transcript_variant	3		ENSP00000463110

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

88288

AN:

151820

Hom.:

26938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.445

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.577

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.570

GnomAD4 exome

AF:

0.532

AC:

727159

AN:

1366508

Hom.:

196082

AF XY:

0.529

AC XY:

356206

AN XY:

673694

show subpopulations

Gnomad4 AFR exome

AF:

0.792

Gnomad4 AMR exome

AF:

0.427

Gnomad4 ASJ exome

AF:

0.446

Gnomad4 EAS exome

AF:

0.447

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.438

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.534

GnomAD4 genome

AF:

0.582

AC:

88394

AN:

151934

Hom.:

26987

Cov.:

AF XY:

0.571

AC XY:

42437

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.776

Gnomad4 AMR

AF:

0.495

Gnomad4 ASJ

AF:

0.445

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.534

Gnomad4 OTH

AF:

0.567

Alfa

AF:

0.385

Hom.:

906

Bravo

AF:

0.594

Asia WGS

AF:

0.455

AC:

1583

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.8

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over