12-121921491-G-GGAGGAGGAGGAGGAGAAA

Position:

• chr12-121921491-G-GGAGGAGGAGGAGGAGAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_144668.6(CFAP251):​c.196_197insAGGAGAAAGAGGAGGAGG​(p.Glu65_Gly66insGluGluLysGluGluGlu) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CFAP251 NM_144668.6 inframe_insertion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.809

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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 12-121921491-G-GGAGGAGGAGGAGGAGAAA is Benign according to our data. Variant chr12-121921491-G-GGAGGAGGAGGAGGAGAAA is described in ClinVar as [Likely_benign]. Clinvar id is 1176969.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP251	NM_144668.6	c.196_197insAGGAGAAAGAGGAGGAGG	p.Glu65_Gly66insGluGluLysGluGluGlu	inframe_insertion	2/22	ENST00000288912.9	NP_653269.3
CFAP251	NM_001178003.2	c.196_197insAGGAGAAAGAGGAGGAGG	p.Glu65_Gly66insGluGluLysGluGluGlu	inframe_insertion	2/18		NP_001171474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP251	ENST00000288912.9	c.196_197insAGGAGAAAGAGGAGGAGG	p.Glu65_Gly66insGluGluLysGluGluGlu	inframe_insertion	2/22	1	NM_144668.6	ENSP00000288912
CFAP251	ENST00000397454.2	c.196_197insAGGAGAAAGAGGAGGAGG	p.Glu65_Gly66insGluGluLysGluGluGlu	inframe_insertion	2/18	1		ENSP00000380595	P1
CFAP251	ENST00000540779.1	n.94_95insAGGAGAAAGAGGAGGAGG		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.00000662 AC: 1 AN: 151118 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1456770 Hom.: 0 Cov.: 63 AF XY: 0.00 AC XY: 0 AN XY: 724420

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000662 AC: 1 AN: 151118 Hom.: 0 Cov.: 0 AF XY: 0.0000136 AC XY: 1 AN XY: 73670

Gnomad4 AFR AF: 0.0000244

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71082910; hg19: chr12-122359397;