rs2587695

Variant names:

• chr2-119564241-A-C
• rs2587695
• NM_001271049.2:c.527+2127A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-119564241-A-C
• chr2-119564241-A-G
• chr2-119564241-A-T

Variant summary

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

The NM_001271049.2(CFAP221):​c.527+2127A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: CFAP221 NM_001271049.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 27 publications found

Genes affected

CFAP221 (HGNC:33720): (cilia and flagella associated protein 221) Predicted to enable calmodulin binding activity. Predicted to be involved in cilium assembly. Predicted to act upstream of or within cerebrospinal fluid circulation; motile cilium assembly; and mucociliary clearance. Predicted to be located in axoneme; extracellular region; and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

CFAP221 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia

  Inheritance: AD, AR Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Ambry Genetics

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 (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP221	NM_001271049.2	c.527+2127A>C		intron_variant	Intron 6 of 23	ENST00000413369.8	NP_001257978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP221	ENST00000413369.8	c.527+2127A>C		intron_variant	Intron 6 of 23	5	NM_001271049.2	ENSP00000393222.2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2587695; hg19: chr2-120321817;