9-20714015-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375567.1(FOCAD):c.-32-1307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,188 control chromosomes in the GnomAD database, including 56,307 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.86 (56307 hom., cov: 32)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.-32-1307C>T		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.-32-1307C>T		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.-32-1307C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130704 AN: 152070 Hom.: 56251 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.871

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.860 AC: 130812 AN: 152188 Hom.: 56307 Cov.: 32 AF XY: 0.860 AC XY: 63962 AN XY: 74398

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.864

Alfa AF: 0.856 Hom.: 108942

Bravo AF: 0.860

Asia WGS AF: 0.772 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	13
Dann	Benign	0.86

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: rs2039391; hg19: chr9-20714014;