Variant 15-81136552-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_173528.4(CFAP161):c.196T>A(p.Tyr66Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

CFAP161
NM_173528.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.30

Variant links:

Genes affected

CFAP161 (HGNC:26782): (cilia and flagella associated protein 161)

CFAP161 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CFAP161	NM_173528.4 linkuse as main transcript	c.196T>A	p.Tyr66Asn	missense_variant	3/7	ENST00000286732.5
CFAP161	NM_001353365.2 linkuse as main transcript	c.196T>A	p.Tyr66Asn	missense_variant	3/6
CFAP161	XM_006720408.3 linkuse as main transcript	c.121T>A	p.Tyr41Asn	missense_variant	4/8
CFAP161	XM_017021963.2 linkuse as main transcript	c.121T>A	p.Tyr41Asn	missense_variant	4/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP161	ENST00000286732.5 linkuse as main transcript	c.196T>A	p.Tyr66Asn	missense_variant	3/7	1	NM_173528.4	P1	Q6P656-1
CFAP161	ENST00000560091.5 linkuse as main transcript	c.121T>A	p.Tyr41Asn	missense_variant	4/5	5
CFAP161	ENST00000561216.1 linkuse as main transcript	c.121T>A	p.Tyr41Asn	missense_variant	4/4	4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000401

AC:

AN:

249564

Hom.:

AF XY:

0.00000739

AC XY:

AN XY:

135398

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000165

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461878

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 22, 2023

The c.196T>A (p.Y66N) alteration is located in exon 3 (coding exon 3) of the CFAP161 gene. This alteration results from a T to A substitution at nucleotide position 196, causing the tyrosine (Y) at amino acid position 66 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.0078

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.19

.;T;T

Eigen

Benign

0.068

Eigen_PC

Benign

-0.060

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.74

T;T;T

M_CAP

Benign

0.028

MetaRNN

Uncertain

0.59

D;D;D

MetaSVM

Benign

-0.59

MutationTaster

Benign

0.56

PROVEAN

Pathogenic

-6.4

D;D;D

REVEL

Uncertain

0.31

Sift

Pathogenic

0.0

D;D;D

Sift4G

Uncertain

0.011

D;D;D

Polyphen

0.99

.;.;D

Vest4

0.54

MutPred

0.66

.;.;Loss of sheet (P = 0.0457);

MVP

0.082

MPC

0.30

ClinPred

0.95

GERP RS

4.2

Varity_R

0.39

gMVP

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over