9-69865524-G-A

Variant names:

• chr9-69865524-G-A
• rs766003
• NM_001010940.3:c.449+7547G>A

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+7547G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,822 control chromosomes in the GnomAD database, including 24,276 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 0.56 (24276 hom., cov: 30)
• Consequence: CFAP95 NM_001010940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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+7547G>A		intron	N/A	NP_001010940.1
	CFAP95	NM_001308084.2		c.449+7547G>A		intron	N/A	NP_001295013.1
	CFAP95	NM_001308085.2		c.152+7547G>A		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+7547G>A		intron	N/A	ENSP00000366402.3
	CFAP95	ENST00000527647.5	TSL:1	c.449+7547G>A		intron	N/A	ENSP00000431855.1
	CFAP95	ENST00000466872.2	TSL:1	n.392+7547G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85244 AN: 151704 Hom.: 24270 Cov.: 30

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.562 AC: 85281 AN: 151822 Hom.: 24276 Cov.: 30 AF XY: 0.560 AC XY: 41533 AN XY: 74188

African (AFR) AF: 0.506 AC: 20934 AN: 41396

American (AMR) AF: 0.548 AC: 8350 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3466

East Asian (EAS) AF: 0.817 AC: 4203 AN: 5146

South Asian (SAS) AF: 0.624 AC: 3000 AN: 4806

European-Finnish (FIN) AF: 0.467 AC: 4918 AN: 10524

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39376 AN: 67926

Other (OTH) AF: 0.596 AC: 1257 AN: 2110

Alfa AF: 0.584 Hom.: 101539

Bravo AF: 0.568

Asia WGS AF: 0.723 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.40
PhyloP100		-0.60
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: rs766003; hg19: chr9-72480440; COSMIC: COSV65874912;