Variant chr9-20720318-GGT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001375567.1(FOCAD):c.133-47_133-46del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,368,524 control chromosomes in the GnomAD database, including 710 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.041 ( 404 hom., cov: 30)

Exomes 𝑓: 0.010 ( 306 hom. )

Consequence

FOCAD
NM_001375567.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.391

Variant links:

Genes affected

FOCAD (HGNC:23377): (focadhesin) Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

FOCAD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-20720318-GGT-G is Benign according to our data. Variant chr9-20720318-GGT-G is described in ClinVar as [Benign]. Clinvar id is 1224232.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1 linkuse as main transcript	c.133-47_133-46del		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11 linkuse as main transcript	c.133-47_133-46del		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5 linkuse as main transcript	c.133-47_133-46del		intron_variant		1		P1

Frequencies

GnomAD3 genomes

AF:

0.0406

AC:

6148

AN:

151566

Hom.:

393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0203

Gnomad ASJ

AF:

0.00635

Gnomad EAS

AF:

0.00985

Gnomad SAS

AF:

0.00374

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000501

Gnomad OTH

AF:

0.0241

GnomAD4 exome

AF:

0.0103

AC:

12485

AN:

1216844

Hom.:

306

AF XY:

0.00963

AC XY:

5838

AN XY:

606200

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.0147

Gnomad4 ASJ exome

AF:

0.0123

Gnomad4 EAS exome

AF:

0.0205

Gnomad4 SAS exome

AF:

0.00908

Gnomad4 FIN exome

AF:

0.00198

Gnomad4 NFE exome

AF:

0.00546

Gnomad4 OTH exome

AF:

0.0167

GnomAD4 genome

AF:

0.0408

AC:

6189

AN:

151680

Hom.:

404

Cov.:

AF XY:

0.0396

AC XY:

2936

AN XY:

74126

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.0203

Gnomad4 ASJ

AF:

0.00635

Gnomad4 EAS

AF:

0.00987

Gnomad4 SAS

AF:

0.00375

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000501

Gnomad4 OTH

AF:

0.0238

Bravo

AF:

0.0465

Asia WGS

AF:

0.0320

AC:

112

AN:

3478

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

GeneDx

Sep 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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