3-113291671-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7

The NM_001164496.2(CFAP44):​c.5451G>A​(p.Ala1817=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,537,272 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 (no stars).

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

CFAP44
NM_001164496.2 synonymous

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.66
Variant links:
Genes affected
CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 3-113291671-C-T is Benign according to our data. Variant chr3-113291671-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3033995.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.66 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFAP44NM_001164496.2 linkuse as main transcriptc.5451G>A p.Ala1817= synonymous_variant 35/35 ENST00000393845.9
LOC127898559NR_183046.1 linkuse as main transcriptn.8087G>A non_coding_transcript_exon_variant 48/48

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFAP44ENST00000393845.9 linkuse as main transcriptc.5451G>A p.Ala1817= synonymous_variant 35/355 NM_001164496.2 P2Q96MT7-2
CFAP44ENST00000484923.1 linkuse as main transcriptn.583G>A non_coding_transcript_exon_variant 2/24
CFAP44ENST00000461734.1 linkuse as main transcriptc.*141G>A 3_prime_UTR_variant, NMD_transcript_variant 10/102
CFAP44ENST00000489244.1 linkuse as main transcriptc.*374G>A 3_prime_UTR_variant, NMD_transcript_variant 4/45

Frequencies

GnomAD3 genomes
AF:
0.000500
AC:
76
AN:
152148
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00154
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
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:
0.000147
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000123
AC:
18
AN:
145780
Hom.:
0
AF XY:
0.000142
AC XY:
11
AN XY:
77504
show subpopulations
Gnomad AFR exome
AF:
0.00102
Gnomad AMR exome
AF:
0.0000406
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000880
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000116
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000112
AC:
155
AN:
1385006
Hom.:
0
Cov.:
34
AF XY:
0.000114
AC XY:
78
AN XY:
683420
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.0000280
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000505
Gnomad4 FIN exome
AF:
0.0000285
Gnomad4 NFE exome
AF:
0.000101
Gnomad4 OTH exome
AF:
0.000103
GnomAD4 genome
AF:
0.000499
AC:
76
AN:
152266
Hom.:
0
Cov.:
32
AF XY:
0.000403
AC XY:
30
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00154
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.000214
Hom.:
0
Bravo
AF:
0.000465

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

CFAP44-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesFeb 22, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
1.9
DANN
Benign
0.79

Splicing

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: rs377654876; hg19: chr3-113010518; API