16-75397932-C-G

Variant names:

• chr16-75397932-C-G
• rs11149824
• NM_006324.3:c.531-2723G>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.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
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006324.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFDP1	NM_006324.3	MANE Select	c.531-2723G>C		intron	N/A	NP_006315.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFDP1	ENST00000283882.4	TSL:1 MANE Select	c.531-2723G>C		intron	N/A	ENSP00000283882.3
	CFDP1	ENST00000566901.5	TSL:1	n.640-2723G>C		intron	N/A
	CFDP1	ENST00000862206.1		c.654-2723G>C		intron	N/A	ENSP00000532265.1

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

African (AFR) AF: 0.337 AC: 13973 AN: 41502

American (AMR) AF: 0.641 AC: 9799 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2080 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2822 AN: 5168

South Asian (SAS) AF: 0.548 AC: 2645 AN: 4826

European-Finnish (FIN) AF: 0.550 AC: 5817 AN: 10580

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

European-Non Finnish (NFE) AF: 0.589 AC: 40055 AN: 68006

Other (OTH) AF: 0.548 AC: 1159 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.61
PhyloP100		-1.2
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: rs11149824; hg19: chr16-75431830;