3-100928905-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABI3BP	NM_001375547.2	c.80-2424G>A		intron_variant	Intron 1 of 67	ENST00000471714.6	NP_001362476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABI3BP	ENST00000471714.6	c.80-2424G>A		intron_variant	Intron 1 of 67	5	NM_001375547.2	ENSP00000420524.2

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

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.880

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.26

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: rs2576377; hg19: chr3-100647749;