rs2865531

Variant names:

• chr16-75356418-T-A
• rs2865531
• NM_006324.3:c.650+38672A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-75356418-T-A
• chr16-75356418-T-C
• chr16-75356418-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 47 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFDP1	NM_006324.3	c.650+38672A>T		intron_variant	Intron 5 of 6	ENST00000283882.4	NP_006315.1
CFDP1	XR_007064846.1	n.930+34962A>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFDP1	ENST00000283882.4	c.650+38672A>T		intron_variant	Intron 5 of 6	1	NM_006324.3	ENSP00000283882.3
CFDP1	ENST00000564793.1	n.161+6457A>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.351 AC: 14564 AN: 41484

American (AMR) AF: 0.641 AC: 9793 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2080 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2829 AN: 5174

South Asian (SAS) AF: 0.549 AC: 2634 AN: 4802

European-Finnish (FIN) AF: 0.549 AC: 5785 AN: 10532

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40022 AN: 67972

Other (OTH) AF: 0.550 AC: 1162 AN: 2112

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
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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: rs2865531; hg19: chr16-75390316;