rs7851363

chr9-20758307-T-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.494+116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 590,904 control chromosomes in the GnomAD database, including 18,059 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (3862 hom., cov: 31)
  • Exomes 𝑓: 0.25 (14197 hom.)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.363

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=-0.87).
• BP6: Variant 9-20758307-T-A is Benign according to our data. Variant chr9-20758307-T-A is described in ClinVar as [Benign]. Clinvar id is 1288052.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.494+116T>A		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.494+116T>A		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.494+116T>A		intron_variant		1		P1
FOCAD	ENST00000604103.1	n.289+116T>A		intron_variant, non_coding_transcript_variant		4
FOCAD	ENST00000605031.5	n.270+116T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32697 AN: 151910 Hom.: 3859 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.246 AC: 107893 AN: 438876 Hom.: 14197 AF XY: 0.251 AC XY: 57774 AN XY: 230452

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.209

Gnomad4 ASJ exome AF: 0.175

Gnomad4 EAS exome AF: 0.0760

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.252

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.234

GnomAD4 genome AF: 0.215 AC: 32712 AN: 152028 Hom.: 3862 Cov.: 31 AF XY: 0.214 AC XY: 15924 AN XY: 74310

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.230

Alfa AF: 0.230 Hom.: 602

Bravo AF: 0.208

Asia WGS AF: 0.182 AC: 631 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.0
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7851363; hg19: chr9-20758306;