16-75432798-G-T

Variant summary

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

The NM_006324.3(CFDP1):c.64+491C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,988 control chromosomes in the GnomAD database, including 21,351 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 (21351 hom., cov: 31)
• Consequence: CFDP1 NM_006324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFDP1	NM_006324.3	c.64+491C>A		intron_variant		ENST00000283882.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFDP1	ENST00000283882.4	c.64+491C>A		intron_variant		1	NM_006324.3	P1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78543 AN: 151870 Hom.: 21334 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.517 AC: 78595 AN: 151988 Hom.: 21351 Cov.: 31 AF XY: 0.517 AC XY: 38408 AN XY: 74282

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.547

Alfa AF: 0.557 Hom.: 9891

Bravo AF: 0.515

Asia WGS AF: 0.520 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.5
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs12917651; hg19: chr16-75466696;