9-69864440-T-C

Variant names:

• chr9-69864440-T-C
• rs1389124
• NM_001010940.3:c.449+6463T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010940.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP95	NM_001010940.3	MANE Select	c.449+6463T>C		intron	N/A	NP_001010940.1
	CFAP95	NM_001308084.2		c.449+6463T>C		intron	N/A	NP_001295013.1
	CFAP95	NM_001308085.2		c.152+6463T>C		intron	N/A	NP_001295014.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP95	ENST00000377197.8	TSL:1 MANE Select	c.449+6463T>C		intron	N/A	ENSP00000366402.3
	CFAP95	ENST00000527647.5	TSL:1	c.449+6463T>C		intron	N/A	ENSP00000431855.1
	CFAP95	ENST00000466872.2	TSL:1	n.392+6463T>C		intron	N/A

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

African (AFR) AF: 0.811 AC: 33614 AN: 41454

American (AMR) AF: 0.837 AC: 12776 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4269 AN: 5164

South Asian (SAS) AF: 0.863 AC: 4156 AN: 4816

European-Finnish (FIN) AF: 0.828 AC: 8744 AN: 10566

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59479 AN: 67996

Other (OTH) AF: 0.864 AC: 1822 AN: 2110

Alfa AF: 0.861 Hom.: 9766

Bravo AF: 0.848

Asia WGS AF: 0.860 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.21
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: rs1389124; hg19: chr9-72479356; COSMIC: COSV65874903;