9-20715278-G-T

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.-32-44G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00659 in 896,400 control chromosomes in the GnomAD database, including 241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.025 (173 hom., cov: 32)
  • Exomes 𝑓: 0.0029 (68 hom.)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.15

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=-0.85).
• BP6: Variant 9-20715278-G-T is Benign according to our data. Variant chr9-20715278-G-T is described in ClinVar as [Benign]. Clinvar id is 1269550.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.-32-44G>T		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.-32-44G>T		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.-32-44G>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3730 AN: 152142 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0114

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000515

Gnomad OTH AF: 0.0196

GnomAD4 exome AF: 0.00291 AC: 2167 AN: 744140 Hom.: 68 Cov.: 10 AF XY: 0.00246 AC XY: 930 AN XY: 378138

Gnomad4 AFR exome AF: 0.0881

Gnomad4 AMR exome AF: 0.00639

Gnomad4 ASJ exome AF: 0.00248

Gnomad4 EAS exome AF: 0.0000339

Gnomad4 SAS exome AF: 0.000281

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000347

Gnomad4 OTH exome AF: 0.00722

GnomAD4 genome AF: 0.0246 AC: 3739 AN: 152260 Hom.: 173 Cov.: 32 AF XY: 0.0232 AC XY: 1728 AN XY: 74450

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.0114

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000515

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0162 Hom.: 14

Bravo AF: 0.0279

Asia WGS AF: 0.00433 AC: 17 AN: 3476

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

Jul 26, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.16
Dann	Benign	0.45

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: rs73436459; hg19: chr9-20715277;