chr9-69865524-G-A

Position:

• chr9-69865524-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP95	NM_001010940.3	c.449+7547G>A		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+7547G>A		intron_variant		1	NM_001010940.3	ENSP00000366402	P1

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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.596

Alfa AF: 0.591 Hom.: 44701

Bravo AF: 0.568

Asia WGS AF: 0.723 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.40

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: rs766003; hg19: chr9-72480440; COSMIC: COSV65874912;