rs2865531

chr16-75356418-T-Achr16-75356418-T-Cchr16-75356418-T-G

Variant summary

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

The NM_006324.3(CFDP1):c.650+38672A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,030 control chromosomes in the GnomAD database, including 21,697 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 (21697 hom., cov: 32)
• Consequence: CFDP1 NM_006324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFDP1	NM_006324.3	c.650+38672A>T		intron_variant		ENST00000283882.4
CFDP1	XR_007064846.1	n.930+34962A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFDP1	ENST00000283882.4	c.650+38672A>T		intron_variant		1	NM_006324.3	P1
CFDP1	ENST00000564793.1	n.161+6457A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79319 AN: 151912 Hom.: 21679 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.522 AC: 79372 AN: 152030 Hom.: 21697 Cov.: 32 AF XY: 0.523 AC XY: 38831 AN XY: 74286

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.550

Alfa AF: 0.440 Hom.: 1320

Bravo AF: 0.518

Asia WGS AF: 0.547 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	12
Dann	Benign	0.93

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: rs2865531; hg19: chr16-75390316;