1-43150666-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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: Benign. The variant received -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.

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>C		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>C		intron	N/A	ENSP00000334415.3	A6NL82
	CFAP144	ENST00000409396.5	TSL:3	c.134-95G>C		intron	N/A	ENSP00000387254.1	B7ZBL7
	CFAP144	ENST00000410048.5	TSL:3	c.50-95G>C		intron	N/A	ENSP00000387249.1	B7ZBL6

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

African (AFR) AF: 0.272 AC: 5922 AN: 21800

American (AMR) AF: 0.0797 AC: 2750 AN: 34512

Ashkenazi Jewish (ASJ) AF: 0.0659 AC: 1428 AN: 21682

East Asian (EAS) AF: 0.00162 AC: 54 AN: 33418

South Asian (SAS) AF: 0.0909 AC: 6238 AN: 68658

European-Finnish (FIN) AF: 0.0380 AC: 1796 AN: 47286

Middle Eastern (MID) AF: 0.0944 AC: 448 AN: 4746

European-Non Finnish (NFE) AF: 0.0471 AC: 30272 AN: 642286

Other (OTH) AF: 0.0657 AC: 2754 AN: 41936

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

African (AFR) AF: 0.267 AC: 11083 AN: 41544

American (AMR) AF: 0.0733 AC: 1121 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3472

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5184

South Asian (SAS) AF: 0.0956 AC: 462 AN: 4832

European-Finnish (FIN) AF: 0.0343 AC: 364 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3093 AN: 68034

Other (OTH) AF: 0.0960 AC: 203 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		0.024
Mutation Taster		=100/0	polymorphism (auto)

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;