rs1475660

Variant names:

• chr9-20756548-G-A
• rs1475660
• NM_001375567.1:c.393-1542G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-20756548-G-A
• chr9-20756548-G-C
• chr9-20756548-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375567.1(FOCAD):​c.393-1542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,058 control chromosomes in the GnomAD database, including 33,278 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 0.66 (33278 hom., cov: 33)
• Consequence: FOCAD NM_001375567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

Genes affected

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

FOCAD Gene-Disease associations (from GenCC):

• liver disease, severe congenital

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOCAD	NM_001375567.1	c.393-1542G>A		intron_variant	Intron 5 of 43	ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11	c.393-1542G>A		intron_variant	Intron 5 of 43	5	NM_001375567.1	ENSP00000344307.6
FOCAD	ENST00000380249.5	c.393-1542G>A		intron_variant	Intron 7 of 45	1		ENSP00000369599.1
FOCAD	ENST00000604103.1	n.188-1542G>A		intron_variant	Intron 2 of 4	4
FOCAD	ENST00000605031.5	n.169-1542G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100065 AN: 151940 Hom.: 33245 Cov.: 33

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.659 AC: 100145 AN: 152058 Hom.: 33278 Cov.: 33 AF XY: 0.659 AC XY: 48973 AN XY: 74324

African (AFR) AF: 0.616 AC: 25536 AN: 41478

American (AMR) AF: 0.601 AC: 9173 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2177 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2584 AN: 5156

South Asian (SAS) AF: 0.710 AC: 3426 AN: 4822

European-Finnish (FIN) AF: 0.746 AC: 7894 AN: 10580

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47315 AN: 67978

Other (OTH) AF: 0.658 AC: 1389 AN: 2110

Alfa AF: 0.669 Hom.: 107245

Bravo AF: 0.641

Asia WGS AF: 0.575 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.072
DANN	Benign	0.19
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1475660; hg19: chr9-20756547;