rs7869694

Variant names:

• chr9-69869781-A-G
• rs7869694
• NM_001010940.3:c.449+11804A>G

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+11804A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,022 control chromosomes in the GnomAD database, including 1,688 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 0.15 (1688 hom., cov: 32)
• Consequence: CFAP95 NM_001010940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP95	NM_001010940.3	c.449+11804A>G		intron_variant	Intron 4 of 5	ENST00000377197.8	NP_001010940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP95	ENST00000377197.8	c.449+11804A>G		intron_variant	Intron 4 of 5	1	NM_001010940.3	ENSP00000366402.3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22263 AN: 151904 Hom.: 1689 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.147 AC: 22274 AN: 152022 Hom.: 1688 Cov.: 32 AF XY: 0.149 AC XY: 11081 AN XY: 74346

African (AFR) AF: 0.151 AC: 6269 AN: 41488

American (AMR) AF: 0.166 AC: 2542 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1369 AN: 5172

South Asian (SAS) AF: 0.157 AC: 756 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1177 AN: 10518

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9221 AN: 67968

Other (OTH) AF: 0.141 AC: 298 AN: 2116

Alfa AF: 0.143 Hom.: 4908

Bravo AF: 0.153

Asia WGS AF: 0.183 AC: 639 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		0.060
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: rs7869694; hg19: chr9-72484697;