7-130434389-G-T

Position:

• chr7-130434389-G-T

Variant summary

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

The NM_018718.3(CEP41):​c.34-6371C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,964 control chromosomes in the GnomAD database, including 20,236 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 0.51 (20236 hom., cov: 32)
• Consequence: CEP41 NM_018718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

CEP41 (HGNC:12370): (centrosomal protein 41) This gene encodes a centrosomal and microtubule-binding protein which is predicted to have two coiled-coil domains and a rhodanese domain. In human retinal pigment epithelial cells the protein localized to centrioles and cilia. Mutations in this gene have been associated with Joubert Syndrome 15; an autosomal recessive ciliopathy and neurological disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

CEP41 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP41	NM_018718.3	c.34-6371C>A		intron_variant		ENST00000223208.10	NP_061188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP41	ENST00000223208.10	c.34-6371C>A		intron_variant		1	NM_018718.3	ENSP00000223208.4

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77927 AN: 151844 Hom.: 20197 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.513 AC: 78021 AN: 151964 Hom.: 20236 Cov.: 32 AF XY: 0.507 AC XY: 37692 AN XY: 74278

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.517

Alfa AF: 0.430 Hom.: 1603

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.14

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: rs6467308; hg19: chr7-130074230;