chr16-75432798-G-T

Variant names:

• chr16-75432798-G-T
• rs12917651
• NM_006324.3:c.64+491C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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]

ENSG00000261717 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFDP1	NM_006324.3	c.64+491C>A		intron_variant	Intron 1 of 6	ENST00000283882.4	NP_006315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4	c.64+491C>A		intron_variant	Intron 1 of 6	1	NM_006324.3	ENSP00000283882.3
ENSG00000261717	ENST00000567194.5	c.236-18103C>A		intron_variant	Intron 2 of 3	2		ENSP00000457654.1

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

African (AFR) AF: 0.344 AC: 14245 AN: 41460

American (AMR) AF: 0.638 AC: 9736 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3468

East Asian (EAS) AF: 0.515 AC: 2662 AN: 5170

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4820

European-Finnish (FIN) AF: 0.536 AC: 5655 AN: 10560

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39948 AN: 67932

Other (OTH) AF: 0.547 AC: 1156 AN: 2114

Alfa AF: 0.560 Hom.: 11222

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
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12917651; hg19: chr16-75466696;