19-32973319-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_152266.5(FAAP24):​c.106+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,612,610 control chromosomes in the GnomAD database, including 26,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2751 hom., cov: 32)
Exomes 𝑓: 0.17 ( 23558 hom. )

Consequence

FAAP24
NM_152266.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0470
Variant links:
Genes affected
FAAP24 (HGNC:28467): (FA core complex associated protein 24) FAAP24 is a component of the Fanconi anemia (FA) core complex (see MIM 227650), which plays a crucial role in DNA damage response (Ciccia et al., 2007 [PubMed 17289582]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 19-32973319-C-T is Benign according to our data. Variant chr19-32973319-C-T is described in ClinVar as [Benign]. Clinvar id is 2688491.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAAP24NM_152266.5 linkc.106+17C>T intron_variant Intron 2 of 4 ENST00000588258.6 NP_689479.1 Q9BTP7A0A0S2Z5V6
FAAP24NM_001300978.2 linkc.-42-741C>T intron_variant Intron 1 of 2 NP_001287907.1 Q9BTP7K7EKQ4
FAAP24XM_005259393.4 linkc.35+17C>T intron_variant Intron 2 of 4 XP_005259450.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAAP24ENST00000588258.6 linkc.106+17C>T intron_variant Intron 2 of 4 1 NM_152266.5 ENSP00000466121.1 Q9BTP7

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27325
AN:
151916
Hom.:
2745
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.246
Gnomad AMI
AF:
0.0824
Gnomad AMR
AF:
0.114
Gnomad ASJ
AF:
0.0805
Gnomad EAS
AF:
0.00270
Gnomad SAS
AF:
0.150
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.182
Gnomad OTH
AF:
0.149
GnomAD3 exomes
AF:
0.147
AC:
36676
AN:
250314
Hom.:
3246
AF XY:
0.148
AC XY:
20031
AN XY:
135340
show subpopulations
Gnomad AFR exome
AF:
0.245
Gnomad AMR exome
AF:
0.0718
Gnomad ASJ exome
AF:
0.0811
Gnomad EAS exome
AF:
0.00153
Gnomad SAS exome
AF:
0.145
Gnomad FIN exome
AF:
0.165
Gnomad NFE exome
AF:
0.181
Gnomad OTH exome
AF:
0.145
GnomAD4 exome
AF:
0.174
AC:
254310
AN:
1460578
Hom.:
23558
Cov.:
36
AF XY:
0.173
AC XY:
125737
AN XY:
726516
show subpopulations
Gnomad4 AFR exome
AF:
0.245
Gnomad4 AMR exome
AF:
0.0760
Gnomad4 ASJ exome
AF:
0.0814
Gnomad4 EAS exome
AF:
0.00103
Gnomad4 SAS exome
AF:
0.151
Gnomad4 FIN exome
AF:
0.166
Gnomad4 NFE exome
AF:
0.188
Gnomad4 OTH exome
AF:
0.157
GnomAD4 genome
AF:
0.180
AC:
27355
AN:
152032
Hom.:
2751
Cov.:
32
AF XY:
0.175
AC XY:
13022
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.246
Gnomad4 AMR
AF:
0.114
Gnomad4 ASJ
AF:
0.0805
Gnomad4 EAS
AF:
0.00290
Gnomad4 SAS
AF:
0.150
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.182
Gnomad4 OTH
AF:
0.147
Alfa
AF:
0.157
Hom.:
379
Bravo
AF:
0.176
Asia WGS
AF:
0.0700
AC:
242
AN:
3478

ClinVar

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

Submissions by phenotype

not specified Benign:1
Jan 24, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
6.4
DANN
Benign
0.47

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.

Other links and lift over

dbSNP: rs73037453; hg19: chr19-33464225; API