Variant 16-75414582-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_006324.3(CFDP1):c.178G>A(p.Ala60Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,603,784 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 22 hom. )

Consequence

CFDP1
NM_006324.3 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.105

Variant links:

Genes affected

CFDP1 (HGNC:1873): (craniofacial development protein 1) Predicted to act upstream of or within several processes, including cell adhesion; negative regulation of fibroblast apoptotic process; and regulation of cell shape. Predicted to be located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]

CFDP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005605638).

BP6

Variant 16-75414582-C-T is Benign according to our data. Variant chr16-75414582-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3038964.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFDP1	NM_006324.3 linkuse as main transcript	c.178G>A	p.Ala60Thr	missense_variant	2/7	ENST00000283882.4	NP_006315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4 linkuse as main transcript	c.178G>A	p.Ala60Thr	missense_variant	2/7	1	NM_006324.3	ENSP00000283882	P1	Q9UEE9-1
CFDP1	ENST00000566901.5 linkuse as main transcript	n.287G>A		non_coding_transcript_exon_variant	2/5	1
CFDP1	ENST00000564286.1 linkuse as main transcript	n.296G>A		non_coding_transcript_exon_variant	2/5	5
CFDP1	ENST00000565646.5 linkuse as main transcript	n.186-1828G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00370

AC:

563

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00740

Gnomad ASJ

AF:

0.00952

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00434

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00381

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00335

AC:

841

AN:

251360

Hom.:

AF XY:

0.00330

AC XY:

448

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00408

Gnomad ASJ exome

AF:

0.00605

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00137

Gnomad FIN exome

AF:

0.00337

Gnomad NFE exome

AF:

0.00396

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00372

AC:

5403

AN:

1451528

Hom.:

Cov.:

AF XY:

0.00371

AC XY:

2683

AN XY:

722954

show subpopulations

Gnomad4 AFR exome

AF:

0.00289

Gnomad4 AMR exome

AF:

0.00423

Gnomad4 ASJ exome

AF:

0.00717

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00137

Gnomad4 FIN exome

AF:

0.00346

Gnomad4 NFE exome

AF:

0.00397

Gnomad4 OTH exome

AF:

0.00378

GnomAD4 genome

AF:

0.00370

AC:

564

AN:

152256

Hom.:

Cov.:

AF XY:

0.00379

AC XY:

282

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00226

Gnomad4 AMR

AF:

0.00739

Gnomad4 ASJ

AF:

0.00952

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00434

Gnomad4 NFE

AF:

0.00381

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00442

Hom.:

Bravo

AF:

0.00407

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00285

AC:

ESP6500AA

AF:

0.00341

AC:

ESP6500EA

AF:

0.00430

AC:

ExAC

AF:

0.00298

AC:

362

EpiCase

AF:

0.00567

EpiControl

AF:

0.00445

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CFDP1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 23, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.025

T;.;.

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.52

T;T;T

M_CAP

Benign

0.0083

MetaRNN

Benign

0.0056

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.2

L;.;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.40

N;N;N

REVEL

Benign

0.068

Sift

Benign

0.31

T;D;D

Sift4G

Benign

0.65

T;.;.

Polyphen

0.0060

B;.;.

Vest4

0.15

MVP

0.49

MPC

0.013

ClinPred

0.0087

GERP RS

2.0

Varity_R

0.028

gMVP

0.032

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