Variant chr6-122781134-G-A details in Genebe, Genetics Data Aggregator

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

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]

FABP7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

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

Synonymous conserved (PhyloP=3.56 with no splicing effect.

BS1

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

High Homozygotes in GnomAdExome4 at 27 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FABP7	NM_001446.5 linkuse as main transcript	c.288G>A	p.Gln96=	synonymous_variant	3/4	ENST00000368444.8
FABP7	NM_001319039.2 linkuse as main transcript	c.288G>A	p.Gln96=	synonymous_variant	3/3
FABP7	NM_001319042.2 linkuse as main transcript	c.276G>A	p.Gln92=	synonymous_variant	3/4
FABP7	NM_001319041.2 linkuse as main transcript	c.*623G>A		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP7	ENST00000368444.8 linkuse as main transcript	c.288G>A	p.Gln96=	synonymous_variant	3/4	1	NM_001446.5	P1	O15540-1
FABP7	ENST00000356535.4 linkuse as main transcript	c.288G>A	p.Gln96=	synonymous_variant	3/3	1			O15540-2

Frequencies

GnomAD3 genomes

AF:

0.00354

AC:

539

AN:

152158

Hom.:

Cov.:

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.:

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.:

Cov.:

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

AF:

0.00353

AC:

537

AN:

152276

Hom.:

Cov.:

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.:

Bravo

AF:

0.00328

Asia WGS

AF:

0.00664

AC:

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 submitter

clinical testing

Invitae

Dec 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over