Variant chr9-20740078-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001375567.1(FOCAD):c.288-158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,990 control chromosomes in the GnomAD database, including 4,393 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4393 hom., cov: 32)

Consequence

FOCAD
NM_001375567.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.134

Variant links:

Genes affected

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

FOCAD links:

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=-0.86).

BP6

Variant 9-20740078-G-A is Benign according to our data. Variant chr9-20740078-G-A is described in ClinVar as [Benign]. Clinvar id is 1262401.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 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.288-158G>A		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
FOCAD	ENST00000338382.11 linkuse as main transcript	c.288-158G>A	intron_variant	5	NM_001375567.1	P1
FOCAD	ENST00000380249.5 linkuse as main transcript	c.288-158G>A	intron_variant	1		P1
FOCAD	ENST00000604103.1 linkuse as main transcript	n.83-158G>A	intron_variant, non_coding_transcript_variant	4
FOCAD	ENST00000605031.5 linkuse as main transcript	n.64-158G>A	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35575

AN:

151872

Hom.:

4385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.0479

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.234

AC:

35604

AN:

151990

Hom.:

4393

Cov.:

AF XY:

0.233

AC XY:

17280

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.222

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.0480

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.256

Hom.:

1017

Bravo

AF:

0.227

Asia WGS

AF:

0.191

AC:

660

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

Jun 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

DANN

Benign

0.52

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