9-20740078-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.134

Genes affected

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

ACMG classification

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	c.288-158G>A		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.288-158G>A		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.288-158G>A		intron_variant		1		P1
FOCAD	ENST00000604103.1	n.83-158G>A		intron_variant, non_coding_transcript_variant		4
FOCAD	ENST00000605031.5	n.64-158G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35575 AN: 151872 Hom.: 4385 Cov.: 32

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.: 32 AF XY: 0.233 AC XY: 17280 AN XY: 74252

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2019

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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

Other links and lift over

dbSNP: rs10115318; hg19: chr9-20740077;