3-100928905-C-T

Variant names:

• chr3-100928905-C-T
• rs2576377
• NM_001375547.2:c.80-2424G>A

Variant summary

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

The NM_001375547.2(ABI3BP):​c.80-2424G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,060 control chromosomes in the GnomAD database, including 57,183 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 0.87 (57183 hom., cov: 31)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABI3BP	NM_001375547.2	MANE Select	c.80-2424G>A		intron	N/A	NP_001362476.1	D3YTG3
	ABI3BP	NM_001375550.1		c.80-2424G>A		intron	N/A	NP_001362479.1
	ABI3BP	NM_001375549.2		c.80-2424G>A		intron	N/A	NP_001362478.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABI3BP	ENST00000471714.6	TSL:5 MANE Select	c.80-2424G>A		intron	N/A	ENSP00000420524.2	D3YTG3
	ABI3BP	ENST00000284322.10	TSL:1	c.80-2424G>A		intron	N/A	ENSP00000284322.6	Q7Z7G0-1
	ABI3BP	ENST00000495063.6	TSL:1	c.80-2424G>A		intron	N/A	ENSP00000433993.2	F6R962

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131641 AN: 151942 Hom.: 57132 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.866 AC: 131752 AN: 152060 Hom.: 57183 Cov.: 31 AF XY: 0.868 AC XY: 64523 AN XY: 74314

African (AFR) AF: 0.872 AC: 36170 AN: 41492

American (AMR) AF: 0.895 AC: 13635 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3177 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5153 AN: 5156

South Asian (SAS) AF: 0.941 AC: 4542 AN: 4828

European-Finnish (FIN) AF: 0.801 AC: 8492 AN: 10596

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57626 AN: 67966

Other (OTH) AF: 0.880 AC: 1854 AN: 2108

Alfa AF: 0.861 Hom.: 6988

Bravo AF: 0.874

Asia WGS AF: 0.963 AC: 3349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.26
PhyloP100		0.35
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: rs2576377; hg19: chr3-100647749;