rs4888378

Variant names:

• chr16-75298143-A-G
• rs4888378
• NM_006324.3:c.810-4101T>C

Variant summary

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

The NM_006324.3(CFDP1):​c.810-4101T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,104 control chromosomes in the GnomAD database, including 22,017 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 0.52 (22017 hom., cov: 33)
• Consequence: CFDP1 NM_006324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 36 publications found

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]

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 (AMR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFDP1	NM_006324.3	c.810-4101T>C		intron_variant	Intron 6 of 6	ENST00000283882.4	NP_006315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4	c.810-4101T>C		intron_variant	Intron 6 of 6	1	NM_006324.3	ENSP00000283882.3
CFDP1	ENST00000562602.1	n.564+3614T>C		intron_variant	Intron 2 of 2	3
CFDP1	ENST00000564793.1	n.321-4101T>C		intron_variant	Intron 2 of 2	3
CFDP1	ENST00000570103.5	n.319-4101T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79581 AN: 151986 Hom.: 22000 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.524 AC: 79631 AN: 152104 Hom.: 22017 Cov.: 33 AF XY: 0.525 AC XY: 39038 AN XY: 74358

African (AFR) AF: 0.337 AC: 13972 AN: 41462

American (AMR) AF: 0.670 AC: 10248 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2807 AN: 5170

South Asian (SAS) AF: 0.547 AC: 2642 AN: 4830

European-Finnish (FIN) AF: 0.553 AC: 5847 AN: 10574

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40340 AN: 67990

Other (OTH) AF: 0.558 AC: 1179 AN: 2114

Alfa AF: 0.578 Hom.: 13137

Bravo AF: 0.523

Asia WGS AF: 0.539 AC: 1877 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	6.5
DANN	Benign	0.76
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4888378; hg19: chr16-75332041;