rs1475660

Positions:

• chr9-20756548-G-A
• chr9-20756548-G-C
• chr9-20756548-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.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

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=-0.95).
• 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/exons	MANE	Protein	UniProt
FOCAD	NM_001375567.1	c.393-1542G>A		intron_variant		ENST00000338382.11	NP_001362496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOCAD	ENST00000338382.11	c.393-1542G>A		intron_variant		5	NM_001375567.1	ENSP00000344307	P1
FOCAD	ENST00000380249.5	c.393-1542G>A		intron_variant		1		ENSP00000369599	P1
FOCAD	ENST00000604103.1	n.188-1542G>A		intron_variant, non_coding_transcript_variant		4
FOCAD	ENST00000605031.5	n.169-1542G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.658

Alfa AF: 0.673 Hom.: 68258

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

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: rs1475660; hg19: chr9-20756547;