NM_001010940.3:c.471A>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001010940.3(CFAP95):​c.471A>C​(p.Ser157Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00475 in 1,613,336 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0040 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0048 (32 hom.)
• Consequence: CFAP95 NM_001010940.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0720
• Publications: 7 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 9-69886859-A-C is Benign according to our data. Variant chr9-69886859-A-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2659245.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.072 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 2 gene

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>C	p.Ser157Ser	synonymous	Exon 5 of 6	NP_001010940.1	Q5VTT2-1
	CFAP95	NM_001308085.2		c.174A>C	p.Ser58Ser	synonymous	Exon 4 of 5	NP_001295014.1
	CFAP95	NM_001308086.2		c.174A>C	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>C	p.Ser157Ser	synonymous	Exon 5 of 6	ENSP00000366402.3	Q5VTT2-1
	CFAP95	ENST00000527647.5	TSL:1	c.450-19095A>C		intron	N/A	ENSP00000431855.1	Q5VTT2-2
	CFAP95	ENST00000466872.2	TSL:1	n.484A>C		non_coding_transcript_exon	Exon 5 of 6

Frequencies

GnomAD3 genomes AF: 0.00395 AC: 602 AN: 152228 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000820

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00617

Gnomad OTH AF: 0.00191

GnomAD2 exomes AF: 0.00561 AC: 1409 AN: 251002 AF XY: 0.00585

Gnomad AFR exome AF: 0.000985

Gnomad AMR exome AF: 0.000174

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0132

Gnomad NFE exome AF: 0.00932

Gnomad OTH exome AF: 0.00327

GnomAD4 exome AF: 0.00483 AC: 7062 AN: 1460990 Hom.: 32 Cov.: 29 AF XY: 0.00477 AC XY: 3465 AN XY: 726812

African (AFR) AF: 0.000807 AC: 27 AN: 33448

American (AMR) AF: 0.000291 AC: 13 AN: 44676

Ashkenazi Jewish (ASJ) AF: 0.0000766 AC: 2 AN: 26112

East Asian (EAS) AF: 0.00 AC: 0 AN: 39646

South Asian (SAS) AF: 0.000603 AC: 52 AN: 86228

European-Finnish (FIN) AF: 0.0131 AC: 699 AN: 53318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5762

European-Non Finnish (NFE) AF: 0.00544 AC: 6047 AN: 1111450

Other (OTH) AF: 0.00368 AC: 222 AN: 60350

GnomAD4 genome AF: 0.00395 AC: 602 AN: 152346 Hom.: 2 Cov.: 33 AF XY: 0.00403 AC XY: 300 AN XY: 74498

African (AFR) AF: 0.000818 AC: 34 AN: 41588

American (AMR) AF: 0.000457 AC: 7 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00617 AC: 420 AN: 68026

Other (OTH) AF: 0.00189 AC: 4 AN: 2116

Alfa AF: 0.00517 Hom.: 4

Bravo AF: 0.00295

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00387

EpiControl AF: 0.00456

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.49
PhyloP100		-0.072
Mutation Taster		=100/0	polymorphism

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: rs138837310; hg19: chr9-72501775;