rs7961894

chr12-121927677-C-T

Variant summary

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

The NM_144668.6(CFAP251):c.747+3687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,180 control chromosomes in the GnomAD database, including 503 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 0.072 (503 hom., cov: 31)
• Consequence: CFAP251 NM_144668.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

Genes affected

CFAP251 (HGNC:28506): (cilia and flagella associated protein 251) This protein encoded by this gene belongs to the WD repeat-containing family of proteins, which function in the formation of protein-protein complexes in a variety of biological pathways. This family member appears to function in the determination of mean platelet volume (MPV), and polymorphisms in this gene have been associated with variance in MPV. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP251	NM_144668.6	c.747+3687C>T		intron_variant		ENST00000288912.9
CFAP251	NM_001178003.2	c.747+3687C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP251	ENST00000288912.9	c.747+3687C>T		intron_variant		1	NM_144668.6
CFAP251	ENST00000397454.2	c.747+3687C>T		intron_variant		1		P1
CFAP251	ENST00000540779.1	n.645+3687C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10981 AN: 152062 Hom.: 503 Cov.: 31

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0721 AC: 10979 AN: 152180 Hom.: 503 Cov.: 31 AF XY: 0.0715 AC XY: 5317 AN XY: 74380

Gnomad4 AFR AF: 0.0197

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0988 Hom.: 1673

Bravo AF: 0.0701

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.2
Dann	Benign	0.38

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: rs7961894; hg19: chr12-122365583;