1-109112908-C-A

Variant names:

• chr1-109112908-C-A
• rs569700390
• NM_001366200.3:c.45+725G>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001366200.3(CFAP276):​c.45+725G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00619 in 131,770 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0062 (6 hom., cov: 32)
• Consequence: CFAP276 NM_001366200.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.705

Genes affected

CFAP276 (HGNC:32331): (cilia and flagella associated protein 276) Predicted to enable heme binding activity and heme transmembrane transporter activity. Predicted to be involved in heme export. Located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 1-109112908-C-A is Benign according to our data. Variant chr1-109112908-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2498411.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP276	NM_001245025.3	c.-229G>T		upstream_gene_variant		ENST00000369948.8	NP_001231954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP276	ENST00000369948.8	c.-229G>T		upstream_gene_variant		2	NM_001245025.3	ENSP00000358964.3

Frequencies

GnomAD3 genomes AF: 0.00619 AC: 815 AN: 131666 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00260

Gnomad AMI AF: 0.0547

Gnomad AMR AF: 0.00802

Gnomad ASJ AF: 0.0186

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00110

Gnomad FIN AF: 0.00120

Gnomad MID AF: 0.00662

Gnomad NFE AF: 0.00757

Gnomad OTH AF: 0.00536

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

GnomAD4 genome AF: 0.00619 AC: 815 AN: 131770 Hom.: 6 Cov.: 32 AF XY: 0.00566 AC XY: 365 AN XY: 64458

Gnomad4 AFR AF: 0.00259

Gnomad4 AMR AF: 0.00801

Gnomad4 ASJ AF: 0.0186

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00110

Gnomad4 FIN AF: 0.00120

Gnomad4 NFE AF: 0.00758

Gnomad4 OTH AF: 0.00531

Alfa AF: 0.00166 Hom.: 0

Bravo AF: 0.00579

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CFAP276: BS1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569700390; hg19: chr1-109655530;