9-20720318-GGT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.391

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 -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	c.133-47_133-46del		intron_variant		ENST00000338382.11

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6148 AN: 151566 Hom.: 393 Cov.: 30

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

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.: 30 AF XY: 0.0396 AC XY: 2936 AN XY: 74126

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 05, 2019

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Computational scores

Source: dbNSFP v4.3

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: rs112284387; hg19: chr9-20720317;