rs142200520

Variant names:

• chr16-75395118-C-A
• rs142200520
• NM_006324.3:c.622G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-75395118-C-A
• chr16-75395118-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006324.3(CFDP1):​c.622G>T​(p.Ala208Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A208P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000089 (0 hom.)
• Consequence: CFDP1 NM_006324.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05370292).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFDP1	NM_006324.3	MANE Select	c.622G>T	p.Ala208Ser	missense	Exon 5 of 7	NP_006315.1	Q9UEE9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFDP1	ENST00000283882.4	TSL:1 MANE Select	c.622G>T	p.Ala208Ser	missense	Exon 5 of 7	ENSP00000283882.3	Q9UEE9-1
	CFDP1	ENST00000566901.5	TSL:1	n.731G>T		non_coding_transcript_exon	Exon 5 of 5
	CFDP1	ENST00000862206.1		c.745G>T	p.Ala249Ser	missense	Exon 6 of 8	ENSP00000532265.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000889 AC: 13 AN: 1461686 Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8 AN XY: 727148

African (AFR) AF: 0.00 AC: 0 AN: 33474

American (AMR) AF: 0.00 AC: 0 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39690

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53384

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000117 AC: 13 AN: 1111892

Other (OTH) AF: 0.00 AC: 0 AN: 60380

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.3
DANN	Benign	0.94
DEOGEN2	Benign	0.023	T
Eigen	Benign	-0.97
Eigen_PC	Benign	-0.95
FATHMM_MKL	Benign	0.041	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.0056	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.96	L
PhyloP100		-0.42
PrimateAI	Benign	0.32	T
PROVEAN	Benign	0.23	N
REVEL	Benign	0.068
Sift	Benign	0.62	T
Sift4G	Benign	0.63	T
Polyphen		0.0	B
Vest4		0.21
MutPred		0.077		Gain of phosphorylation at A208 (P = 0.0148)
MVP		0.37
MPC		0.013
ClinPred		0.039	T
GERP RS		-0.91
PromoterAI		-0.012	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.024
gMVP		0.26
Mutation Taster		=94/6	polymorphism

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: rs142200520; hg19: chr16-75429016;