rs2055056

Positions:

• chr8-95265842-T-C

Variant summary

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

The NM_177965.4(CFAP418):​c.156-2068A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 152,304 control chromosomes in the GnomAD database, including 592 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 0.072 (592 hom., cov: 32)
• Consequence: CFAP418 NM_177965.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

CFAP418 (HGNC:27232): (cilia and flagella associated protein 418) This gene encodes a ubiquitously expressed protein of unknown function. It has high levels of mRNA expression in the brain, heart, and retina and the protein co-localizes with polyglutamylated tubulin at the base of the primary cilium in human retinal pigment epithelial cells. Mutations in this gene have been associated with autosomal recessive cone-rod dystrophy (arCRD) and retinitis pigmentosa (arRP). [provided by RefSeq, Mar 2012]

CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418	NM_177965.4	c.156-2068A>G		intron_variant		ENST00000286688.6	NP_808880.1
CFAP418	NM_001363260.1	c.156-2068A>G		intron_variant			NP_001350189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418	ENST00000286688.6	c.156-2068A>G		intron_variant		1	NM_177965.4	ENSP00000286688	P1
CFAP418-AS1	ENST00000517655.1	n.521+60530T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10982 AN: 152186 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0722 AC: 10995 AN: 152304 Hom.: 592 Cov.: 32 AF XY: 0.0717 AC XY: 5342 AN XY: 74486

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.00501

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.0583 Hom.: 50

Bravo AF: 0.0821

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.70

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: rs2055056; hg19: chr8-96278070;