chr3-100872081-C-T

Variant names:

• chr3-100872081-C-T
• rs9833094
• NM_001375547.2:c.910+2760G>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.910+2760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,998 control chromosomes in the GnomAD database, including 8,895 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 0.34 (8895 hom., cov: 32)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 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.910+2760G>A		intron	N/A	NP_001362476.1
	ABI3BP	NM_001375550.1		c.910+2760G>A		intron	N/A	NP_001362479.1
	ABI3BP	NM_001375549.2		c.910+2760G>A		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.910+2760G>A		intron	N/A	ENSP00000420524.2
	ABI3BP	ENST00000284322.10	TSL:1	c.910+2760G>A		intron	N/A	ENSP00000284322.6
	ABI3BP	ENST00000495063.6	TSL:1	c.910+2760G>A		intron	N/A	ENSP00000433993.2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51185 AN: 151880 Hom.: 8875 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.337 AC: 51239 AN: 151998 Hom.: 8895 Cov.: 32 AF XY: 0.339 AC XY: 25160 AN XY: 74270

African (AFR) AF: 0.295 AC: 12224 AN: 41464

American (AMR) AF: 0.399 AC: 6090 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5152

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4814

European-Finnish (FIN) AF: 0.335 AC: 3534 AN: 10554

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24019 AN: 67968

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.347 Hom.: 26347

Bravo AF: 0.341

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.71
PhyloP100		-0.30
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: rs9833094; hg19: chr3-100590925;