rs12336110

Positions:

• chr9-20688118-G-A
• chr9-20688118-G-T

Variant summary

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

The NM_001375567.1(FOCAD):​c.-33+3825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,128 control chromosomes in the GnomAD database, including 3,373 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 0.20 (3373 hom., cov: 32)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOCAD	NM_001375567.1	c.-33+3825G>A		intron_variant		ENST00000338382.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOCAD	ENST00000338382.11	c.-33+3825G>A		intron_variant		5	NM_001375567.1	P1
FOCAD	ENST00000380249.5	c.-77-6402G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30991 AN: 152010 Hom.: 3352 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.204 AC: 31049 AN: 152128 Hom.: 3373 Cov.: 32 AF XY: 0.201 AC XY: 14954 AN XY: 74382

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.186

Alfa AF: 0.193 Hom.: 741

Bravo AF: 0.207

Asia WGS AF: 0.158 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.34

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: rs12336110; hg19: chr9-20688117;