rs12330531

Variant names:

• chr3-100870099-T-A
• rs12330531
• NM_001375547.2:c.911-3143A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-100870099-T-A
• chr3-100870099-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375547.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABI3BP	NM_001375547.2	MANE Select	c.911-3143A>T		intron	N/A	NP_001362476.1
	ABI3BP	NM_001375550.1		c.911-3143A>T		intron	N/A	NP_001362479.1
	ABI3BP	NM_001375549.2		c.911-3143A>T		intron	N/A	NP_001362478.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABI3BP	ENST00000471714.6	TSL:5 MANE Select	c.911-3143A>T		intron	N/A	ENSP00000420524.2
	ABI3BP	ENST00000284322.10	TSL:1	c.911-3143A>T		intron	N/A	ENSP00000284322.6
	ABI3BP	ENST00000495063.6	TSL:1	c.911-3143A>T		intron	N/A	ENSP00000433993.2

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

African (AFR) AF: 0.409 AC: 16931 AN: 41400

American (AMR) AF: 0.415 AC: 6347 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3464

East Asian (EAS) AF: 0.316 AC: 1632 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3551 AN: 10574

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24159 AN: 67970

Other (OTH) AF: 0.361 AC: 764 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.61
PhyloP100		-0.36
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: rs12330531; hg19: chr3-100588943;