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GeneBe

6-122781134-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_001446.5(FABP7):c.288G>A(p.Gln96=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0051 in 1,613,930 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0053 ( 27 hom. )

Consequence

FABP7
NM_001446.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.56
Variant links:
Genes affected
FABP7 (HGNC:3562): (fatty acid binding protein 7) The gene encodes a small, highly conserved cytoplasmic protein that bind long-chain fatty acids and other hydrophobic ligands. The encoded protein is important in the establishment of the radial glial fiber in the developing brain. Alternative splicing and promoter usage results in multiple transcript variants encoding different isoforms. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-122781134-G-A is Benign according to our data. Variant chr6-122781134-G-A is described in ClinVar as [Benign]. Clinvar id is 774070.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=3.56 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00527 (7697/1461654) while in subpopulation SAS AF= 0.0168 (1445/86244). AF 95% confidence interval is 0.016. There are 27 homozygotes in gnomad4_exome. There are 4117 alleles in male gnomad4_exome subpopulation. Median coverage is 31. 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 GnomAdExome at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FABP7NM_001446.5 linkuse as main transcriptc.288G>A p.Gln96= synonymous_variant 3/4 ENST00000368444.8
FABP7NM_001319039.2 linkuse as main transcriptc.288G>A p.Gln96= synonymous_variant 3/3
FABP7NM_001319042.2 linkuse as main transcriptc.276G>A p.Gln92= synonymous_variant 3/4
FABP7NM_001319041.2 linkuse as main transcriptc.*623G>A 3_prime_UTR_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FABP7ENST00000368444.8 linkuse as main transcriptc.288G>A p.Gln96= synonymous_variant 3/41 NM_001446.5 P1O15540-1
FABP7ENST00000356535.4 linkuse as main transcriptc.288G>A p.Gln96= synonymous_variant 3/31 O15540-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00354
AC:
539
AN:
152158
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000579
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00478
Gnomad ASJ
AF:
0.0141
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0130
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00456
Gnomad OTH
AF:
0.00719
GnomAD3 exomes
AF:
0.00558
AC:
1402
AN:
251340
Hom.:
7
AF XY:
0.00626
AC XY:
851
AN XY:
135834
show subpopulations
Gnomad AFR exome
AF:
0.000923
Gnomad AMR exome
AF:
0.00304
Gnomad ASJ exome
AF:
0.0160
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0166
Gnomad FIN exome
AF:
0.000555
Gnomad NFE exome
AF:
0.00485
Gnomad OTH exome
AF:
0.00799
GnomAD4 exome
AF:
0.00527
AC:
7697
AN:
1461654
Hom.:
27
Cov.:
31
AF XY:
0.00566
AC XY:
4117
AN XY:
727114
show subpopulations
Gnomad4 AFR exome
AF:
0.000866
Gnomad4 AMR exome
AF:
0.00295
Gnomad4 ASJ exome
AF:
0.0157
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0168
Gnomad4 FIN exome
AF:
0.000543
Gnomad4 NFE exome
AF:
0.00470
Gnomad4 OTH exome
AF:
0.00585
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00353
AC:
537
AN:
152276
Hom.:
1
Cov.:
33
AF XY:
0.00356
AC XY:
265
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.000577
Gnomad4 AMR
AF:
0.00477
Gnomad4 ASJ
AF:
0.0141
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0128
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00456
Gnomad4 OTH
AF:
0.00664
Alfa
AF:
0.00491
Hom.:
2
Bravo
AF:
0.00328
Asia WGS
AF:
0.00664
AC:
23
AN:
3478
EpiCase
AF:
0.00715
EpiControl
AF:
0.00445

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 testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
8.6
Dann
Benign
0.53

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: rs12211883; hg19: chr6-123102279; API