9-69864440-T-C

Position:

• chr9-69864440-T-C

Variant summary

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

The NM_001010940.3(CFAP95):​c.449+6463T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,052 control chromosomes in the GnomAD database, including 54,777 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 0.85 (54777 hom., cov: 30)
• Consequence: CFAP95 NM_001010940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

Genes affected

CFAP95 (HGNC:31422): (cilia and flagella associated protein 95) Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP95	NM_001010940.3	c.449+6463T>C		intron_variant		ENST00000377197.8	NP_001010940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP95	ENST00000377197.8	c.449+6463T>C		intron_variant		1	NM_001010940.3	ENSP00000366402	P1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128880 AN: 151934 Hom.: 54732 Cov.: 30

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.848 AC: 128981 AN: 152052 Hom.: 54777 Cov.: 30 AF XY: 0.846 AC XY: 62830 AN XY: 74300

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.864

Alfa AF: 0.863 Hom.: 9517

Bravo AF: 0.848

Asia WGS AF: 0.860 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
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: rs1389124; hg19: chr9-72479356; COSMIC: COSV65874903;