NM_001010940.3:c.471A>G

Variant names:

• chr9-69886859-A-G
• rs138837310
• NM_001010940.3:c.471A>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001010940.3(CFAP95):​c.471A>G​(p.Ser157Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S157S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CFAP95 NM_001010940.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 0 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=-0.072 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP95	NM_001010940.3	MANE Select	c.471A>G	p.Ser157Ser	synonymous	Exon 5 of 6	NP_001010940.1	Q5VTT2-1
	CFAP95	NM_001308085.2		c.174A>G	p.Ser58Ser	synonymous	Exon 4 of 5	NP_001295014.1
	CFAP95	NM_001308086.2		c.174A>G	p.Ser58Ser	synonymous	Exon 4 of 6	NP_001295015.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP95	ENST00000377197.8	TSL:1 MANE Select	c.471A>G	p.Ser157Ser	synonymous	Exon 5 of 6	ENSP00000366402.3	Q5VTT2-1
	CFAP95	ENST00000527647.5	TSL:1	c.450-19095A>G		intron	N/A	ENSP00000431855.1	Q5VTT2-2
	CFAP95	ENST00000466872.2	TSL:1	n.484A>G		non_coding_transcript_exon	Exon 5 of 6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.56
DANN	Benign	0.49
PhyloP100		-0.072

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs138837310; hg19: chr9-72501775;