rs475093

Positions:

• chr1-43150666-G-C

Variant summary

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

The NM_001101376.3(CFAP144):​c.134-95G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 1,068,632 control chromosomes in the GnomAD database, including 3,938 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 0.11 (1665 hom., cov: 32)
  • Exomes 𝑓: 0.056 (2273 hom.)
• Consequence: CFAP144 NM_001101376.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP144	NM_001101376.3	c.134-95G>C		intron_variant		ENST00000335282.5	NP_001094846.2
CFAP144	XM_005270875.6	c.134-95G>C		intron_variant			XP_005270932.1
CFAP144	XM_005270876.5	c.50-95G>C		intron_variant			XP_005270933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP144	ENST00000335282.5	c.134-95G>C		intron_variant		2	NM_001101376.3	ENSP00000334415.3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16620 AN: 152190 Hom.: 1657 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0970

GnomAD4 exome AF: 0.0564 AC: 51662 AN: 916324 Hom.: 2273 AF XY: 0.0574 AC XY: 27012 AN XY: 470378

Gnomad4 AFR exome AF: 0.272

Gnomad4 AMR exome AF: 0.0797

Gnomad4 ASJ exome AF: 0.0659

Gnomad4 EAS exome AF: 0.00162

Gnomad4 SAS exome AF: 0.0909

Gnomad4 FIN exome AF: 0.0380

Gnomad4 NFE exome AF: 0.0471

Gnomad4 OTH exome AF: 0.0657

GnomAD4 genome AF: 0.109 AC: 16654 AN: 152308 Hom.: 1665 Cov.: 32 AF XY: 0.108 AC XY: 8018 AN XY: 74484

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.0733

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0455

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0846 Hom.: 131

Bravo AF: 0.119

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.53

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: rs475093; hg19: chr1-43616337;