12-96660124-T-C

Variant names:

• chr12-96660124-T-C
• rs11108625
• NM_001306084.2:c.5460+1778T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP54	NM_001306084.2	c.5460+1778T>C		intron_variant	Intron 38 of 67	ENST00000524981.9	NP_001293013.1
CFAP54	NM_001367885.1	c.5460+1778T>C		intron_variant	Intron 38 of 68		NP_001354814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP54	ENST00000524981.9	c.5460+1778T>C		intron_variant	Intron 38 of 67	5	NM_001306084.2	ENSP00000431759.5
CFAP54	ENST00000637336.1	c.2175+1778T>C		intron_variant	Intron 15 of 45	5		ENSP00000490000.1
CFAP54	ENST00000342887.1	n.813+1778T>C		intron_variant	Intron 5 of 26	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

African (AFR) AF: 0.189 AC: 7848 AN: 41512

American (AMR) AF: 0.0988 AC: 1511 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0997 AC: 480 AN: 4816

European-Finnish (FIN) AF: 0.0761 AC: 808 AN: 10612

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7554 AN: 68008

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.112 Hom.: 2024

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
PhyloP100		-1.0
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: rs11108625; hg19: chr12-97053902;