16-75397932-C-G

Position:

• chr16-75397932-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006324.3(CFDP1):​c.531-2723G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,152 control chromosomes in the GnomAD database, including 21,519 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 (21519 hom., cov: 33)
• Consequence: CFDP1 NM_006324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFDP1	NM_006324.3	c.531-2723G>C		intron_variant		ENST00000283882.4	NP_006315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4	c.531-2723G>C		intron_variant		1	NM_006324.3	ENSP00000283882.3
CFDP1	ENST00000566901.5	n.640-2723G>C		intron_variant		1
CFDP1	ENST00000565646.5	n.534-2723G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78797 AN: 152034 Hom.: 21500 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.518 AC: 78851 AN: 152152 Hom.: 21519 Cov.: 33 AF XY: 0.519 AC XY: 38603 AN XY: 74362

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.548

Alfa AF: 0.438 Hom.: 1322

Bravo AF: 0.514

Asia WGS AF: 0.547 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.61

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

Other links and lift over

dbSNP: rs11149824; hg19: chr16-75431830;