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GeneBe

4-88732091-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014883.4(FAM13A):c.2754C>T(p.Asp918=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,613,850 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0060 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00094 ( 9 hom. )

Consequence

FAM13A
NM_014883.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.306
Variant links:
Genes affected
FAM13A (HGNC:19367): (family with sequence similarity 13 member A) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-88732091-G-A is Benign according to our data. Variant chr4-88732091-G-A is described in ClinVar as [Benign]. Clinvar id is 719801.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.306 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00595 (906/152236) while in subpopulation AFR AF= 0.0201 (834/41542). AF 95% confidence interval is 0.0189. There are 8 homozygotes in gnomad4. There are 421 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FAM13ANM_014883.4 linkuse as main transcriptc.2754C>T p.Asp918= synonymous_variant 22/24 ENST00000264344.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FAM13AENST00000264344.10 linkuse as main transcriptc.2754C>T p.Asp918= synonymous_variant 22/245 NM_014883.4 P1O94988-4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00594
AC:
904
AN:
152118
Hom.:
8
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0201
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00196
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00479
GnomAD3 exomes
AF:
0.00208
AC:
523
AN:
251148
Hom.:
4
AF XY:
0.00164
AC XY:
223
AN XY:
135746
show subpopulations
Gnomad AFR exome
AF:
0.0227
Gnomad AMR exome
AF:
0.00107
Gnomad ASJ exome
AF:
0.00477
Gnomad EAS exome
AF:
0.000435
Gnomad SAS exome
AF:
0.000523
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000308
Gnomad OTH exome
AF:
0.00163
GnomAD4 exome
AF:
0.000943
AC:
1379
AN:
1461614
Hom.:
9
Cov.:
30
AF XY:
0.000898
AC XY:
653
AN XY:
727118
show subpopulations
Gnomad4 AFR exome
AF:
0.0254
Gnomad4 AMR exome
AF:
0.00116
Gnomad4 ASJ exome
AF:
0.00471
Gnomad4 EAS exome
AF:
0.000277
Gnomad4 SAS exome
AF:
0.000429
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000132
Gnomad4 OTH exome
AF:
0.00215
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00595
AC:
906
AN:
152236
Hom.:
8
Cov.:
32
AF XY:
0.00566
AC XY:
421
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.0201
Gnomad4 AMR
AF:
0.00196
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00474
Alfa
AF:
0.00254
Hom.:
4
Bravo
AF:
0.00675
Asia WGS
AF:
0.00202
AC:
7
AN:
3478
EpiCase
AF:
0.000382
EpiControl
AF:
0.000712

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeAug 22, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
8.2
Dann
Benign
0.81
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs79098511; hg19: chr4-89653242; API