rs12330531

chr3-100870099-T-Achr3-100870099-T-G

Variant summary

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

The NM_001375547.2(ABI3BP):c.911-3143A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,004 control chromosomes in the GnomAD database, including 10,673 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 0.37 (10673 hom., cov: 32)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

ABI3BP (HGNC:17265): (ABI family member 3 binding protein) Predicted to enable actin filament binding activity and glycosaminoglycan binding activity. Predicted to be involved in regulation of actin cytoskeleton reorganization; regulation of dendritic spine morphogenesis; and regulation of postsynaptic density assembly. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in extracellular space. Colocalizes with collagen-containing extracellular matrix. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABI3BP	NM_001375547.2	c.911-3143A>T		intron_variant		ENST00000471714.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABI3BP	ENST00000471714.6	c.911-3143A>T		intron_variant		5	NM_001375547.2	A2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56326 AN: 151886 Hom.: 10644 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.371 AC: 56395 AN: 152004 Hom.: 10673 Cov.: 32 AF XY: 0.371 AC XY: 27595 AN XY: 74284

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.361

Alfa AF: 0.354 Hom.: 1195

Bravo AF: 0.379

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.2
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: rs12330531; hg19: chr3-100588943;