9-69834079-C-T

Position:

• chr9-69834079-C-T

Variant summary

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

The NM_001010940.3(CFAP95):​c.153-10438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,196 control chromosomes in the GnomAD database, including 862 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 0.099 (862 hom., cov: 32)
• Consequence: CFAP95 NM_001010940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP95	NM_001010940.3	c.153-10438C>T		intron_variant		ENST00000377197.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP95	ENST00000377197.8	c.153-10438C>T		intron_variant		1	NM_001010940.3	P1

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15117 AN: 152078 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0994 AC: 15129 AN: 152196 Hom.: 862 Cov.: 32 AF XY: 0.101 AC XY: 7518 AN XY: 74418

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.00869

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.111 Hom.: 1350

Bravo AF: 0.0916

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.78

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: rs10521434; hg19: chr9-72448995;