NM_001010940.3:c.153-10438C>T

Variant names:

• chr9-69834079-C-T
• rs10521434
• NM_001010940.3:c.153-10438C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.82).
• 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 rank	MANE	Protein	UniProt
CFAP95	NM_001010940.3	c.153-10438C>T		intron_variant	Intron 1 of 5	ENST00000377197.8	NP_001010940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP95	ENST00000377197.8	c.153-10438C>T		intron_variant	Intron 1 of 5	1	NM_001010940.3	ENSP00000366402.3

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

African (AFR) AF: 0.0679 AC: 2820 AN: 41540

American (AMR) AF: 0.0859 AC: 1311 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3468

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5180

South Asian (SAS) AF: 0.185 AC: 890 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1518 AN: 10602

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8005 AN: 68002

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.109 Hom.: 1658

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
PhyloP100		-0.26
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: rs10521434; hg19: chr9-72448995;