chr9-20720600-A-C

Position:

• chr9-20720600-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001375567.1(FOCAD):​c.287+66A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 1,520,574 control chromosomes in the GnomAD database, including 617,147 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.92 (65099 hom., cov: 31)
  • Exomes 𝑓: 0.90 (552048 hom.)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.736

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 9-20720600-A-C is Benign according to our data. Variant chr9-20720600-A-C is described in ClinVar as [Benign]. Clinvar id is 1247067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOCAD	NM_001375567.1	c.287+66A>C		intron_variant		ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11	c.287+66A>C		intron_variant		5	NM_001375567.1	ENSP00000344307	P1
FOCAD	ENST00000380249.5	c.287+66A>C		intron_variant		1		ENSP00000369599	P1

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140394 AN: 152082 Hom.: 65036 Cov.: 31

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.941

GnomAD4 exome AF: 0.897 AC: 1228066 AN: 1368374 Hom.: 552048 AF XY: 0.897 AC XY: 609321 AN XY: 679120

Gnomad4 AFR exome AF: 0.984

Gnomad4 AMR exome AF: 0.958

Gnomad4 ASJ exome AF: 0.954

Gnomad4 EAS exome AF: 0.745

Gnomad4 SAS exome AF: 0.892

Gnomad4 FIN exome AF: 0.906

Gnomad4 NFE exome AF: 0.896

Gnomad4 OTH exome AF: 0.908

GnomAD4 genome AF: 0.923 AC: 140511 AN: 152200 Hom.: 65099 Cov.: 31 AF XY: 0.922 AC XY: 68613 AN XY: 74398

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.934

Alfa AF: 0.916 Hom.: 9341

Bravo AF: 0.928

Asia WGS AF: 0.799 AC: 2776 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.90
CADD	Benign	0.57
DANN	Benign	0.59

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: rs4977898; hg19: chr9-20720599;