16-75375083-T-C

Variant names:

• chr16-75375083-T-C
• rs11646677
• NM_006324.3:c.650+20007A>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+20007A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,222 control chromosomes in the GnomAD database, including 20,234 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 0.50 (20234 hom., cov: 30)
• Consequence: CFDP1 NM_006324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFDP1	NM_006324.3	c.650+20007A>G		intron_variant	Intron 5 of 6	ENST00000283882.4	NP_006315.1
CFDP1	XM_011522814.3	c.651-2515A>G		intron_variant	Intron 5 of 5		XP_011521116.1
CFDP1	XR_007064846.1	n.930+16297A>G		intron_variant	Intron 6 of 6
CFDP1	XR_007064847.1	n.1045+1566A>G		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4	c.650+20007A>G		intron_variant	Intron 5 of 6	1	NM_006324.3	ENSP00000283882.3
CFDP1	ENST00000612761.1	c.30-2515A>G		intron_variant	Intron 1 of 1	3		ENSP00000481200.1
CFDP1	ENST00000569341.1	n.*117-2515A>G		intron_variant	Intron 2 of 2	3		ENSP00000462862.1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75554 AN: 151108 Hom.: 20222 Cov.: 30

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.500 AC: 75599 AN: 151222 Hom.: 20234 Cov.: 30 AF XY: 0.501 AC XY: 36962 AN XY: 73830

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.526

Alfa AF: 0.397 Hom.: 1105

Bravo AF: 0.496

Asia WGS AF: 0.531 AC: 1841 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.3
DANN	Benign	0.94

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: rs11646677; hg19: chr16-75408981;