chr3-119706843-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_033364.4(CFAP91):ā€‹c.159T>Cā€‹(p.His53His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.00011 ( 0 hom., cov: 30)
Exomes š‘“: 0.00011 ( 0 hom. )

Consequence

CFAP91
NM_033364.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0280
Variant links:
Genes affected
CFAP91 (HGNC:24010): (cilia and flagella associated protein 91) Predicted to be involved in cilium movement. Predicted to be located in axoneme and motile cilium. Predicted to colocalize with radial spoke stalk. Implicated in spermatogenic failure 51. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 3-119706843-T-C is Benign according to our data. Variant chr3-119706843-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3025363.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.028 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CFAP91NM_033364.4 linkuse as main transcriptc.159T>C p.His53His synonymous_variant 2/18 ENST00000273390.9 NP_203528.3 Q7Z4T9-7
CFAP91NM_001320316.2 linkuse as main transcriptc.99T>C p.His33His synonymous_variant 2/18 NP_001307245.2 Q7Z4T9
CFAP91NM_001320317.2 linkuse as main transcriptc.16-561T>C intron_variant NP_001307246.2 Q7Z4T9-3
CFAP91NM_001320318.2 linkuse as main transcriptc.-19-1748T>C intron_variant NP_001307247.2 Q7Z4T9-6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CFAP91ENST00000273390.9 linkuse as main transcriptc.159T>C p.His53His synonymous_variant 2/181 NM_033364.4 ENSP00000273390.5 Q7Z4T9-7
ENSG00000285585ENST00000648112.1 linkuse as main transcriptc.159T>C p.His53His synonymous_variant 2/18 ENSP00000497876.1

Frequencies

GnomAD3 genomes
AF:
0.000105
AC:
16
AN:
151670
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000155
AC:
39
AN:
251446
Hom.:
0
AF XY:
0.000147
AC XY:
20
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000139
Gnomad NFE exome
AF:
0.000290
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000112
AC:
164
AN:
1461712
Hom.:
0
Cov.:
29
AF XY:
0.000124
AC XY:
90
AN XY:
727162
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000187
Gnomad4 NFE exome
AF:
0.000129
Gnomad4 OTH exome
AF:
0.000149
GnomAD4 genome
AF:
0.000105
AC:
16
AN:
151670
Hom.:
0
Cov.:
30
AF XY:
0.0000945
AC XY:
7
AN XY:
74036
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000213
Hom.:
0
Bravo
AF:
0.0000718
EpiCase
AF:
0.000218
EpiControl
AF:
0.0000593

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2024CFAP91: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
5.5
DANN
Benign
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs368173878; hg19: chr3-119425690; API