1-43150666-G-A

Variant names:

• chr1-43150666-G-A
• rs475093
• NM_001101376.3:c.134-95G>A

Variant summary

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

The NM_001101376.3(CFAP144):​c.134-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 916,822 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000044 (0 hom.)
• Consequence: CFAP144 NM_001101376.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 0 publications found

Genes affected

CFAP144 (HGNC:34347): (cilia and flagella associated protein 144) Predicted to be located in centrosome and ciliary basal body. Predicted to be active in ciliary base. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001101376.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP144	NM_001101376.3	MANE Select	c.134-95G>A		intron	N/A	NP_001094846.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP144	ENST00000335282.5	TSL:2 MANE Select	c.134-95G>A		intron	N/A	ENSP00000334415.3	A6NL82
	CFAP144	ENST00000409396.5	TSL:3	c.134-95G>A		intron	N/A	ENSP00000387254.1	B7ZBL7
	CFAP144	ENST00000410048.5	TSL:3	c.50-95G>A		intron	N/A	ENSP00000387249.1	B7ZBL6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000436 AC: 4 AN: 916822 Hom.: 0 AF XY: 0.00000212 AC XY: 1 AN XY: 470634

African (AFR) AF: 0.00 AC: 0 AN: 21846

American (AMR) AF: 0.00 AC: 0 AN: 34528

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21688

East Asian (EAS) AF: 0.00 AC: 0 AN: 33420

South Asian (SAS) AF: 0.00 AC: 0 AN: 68692

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47294

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4752

European-Non Finnish (NFE) AF: 0.00000622 AC: 4 AN: 642632

Other (OTH) AF: 0.00 AC: 0 AN: 41970

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		0.024

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: rs475093; hg19: chr1-43616337;