rs11108625

Positions:

• chr12-96660124-T-C

Variant summary

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

The NM_001306084.2(CFAP54):​c.5460+1778T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,208 control chromosomes in the GnomAD database, including 1,254 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 0.12 (1254 hom., cov: 32)
• Consequence: CFAP54 NM_001306084.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

CFAP54 (HGNC:26456): (cilia and flagella associated protein 54) Predicted to be involved in cilium assembly; cilium movement involved in cell motility; and spermatogenesis. Predicted to act upstream of or within cerebrospinal fluid circulation; motile cilium assembly; and mucociliary clearance. Predicted to be located in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

CFAP54 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP54	NM_001306084.2	c.5460+1778T>C		intron_variant		ENST00000524981.9	NP_001293013.1
CFAP54	NM_001367885.1	c.5460+1778T>C		intron_variant			NP_001354814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP54	ENST00000524981.9	c.5460+1778T>C		intron_variant		5	NM_001306084.2	ENSP00000431759.5
CFAP54	ENST00000637336.1	c.2175+1778T>C		intron_variant		5		ENSP00000490000.1
CFAP54	ENST00000342887.1	n.813+1778T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18737 AN: 152090 Hom.: 1242 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.123 AC: 18777 AN: 152208 Hom.: 1254 Cov.: 32 AF XY: 0.121 AC XY: 9018 AN XY: 74416

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.106

Alfa AF: 0.111 Hom.: 1438

Bravo AF: 0.126

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.55

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: rs11108625; hg19: chr12-97053902;