chr9-20821288-C-T

Position:

• chr9-20821288-C-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.1793+217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,026 control chromosomes in the GnomAD database, including 55,136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.85 (55136 hom., cov: 31)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.246

Genes affected

FOCAD (HGNC:23377): (focadhesin) Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

FOCAD (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 9-20821288-C-T is Benign according to our data. Variant chr9-20821288-C-T is described in ClinVar as [Benign]. Clinvar id is 1294440.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOCAD	NM_001375567.1	c.1793+217C>T		intron_variant		ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11	c.1793+217C>T		intron_variant		5	NM_001375567.1	ENSP00000344307.6

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129259 AN: 151910 Hom.: 55088 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.851 AC: 129362 AN: 152026 Hom.: 55136 Cov.: 31 AF XY: 0.853 AC XY: 63342 AN XY: 74282

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.852

Alfa AF: 0.832 Hom.: 50751

Bravo AF: 0.852

Asia WGS AF: 0.783 AC: 2710 AN: 3460

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	-0.95
CADD	Benign	5.3
DANN	Benign	0.61

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: rs1556475; hg19: chr9-20821287;