chr3-100780477-C-A

Variant names:

• chr3-100780477-C-A
• rs7613610
• NM_001375547.2:c.4163-268G>T

Variant summary

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

The NM_001375547.2(ABI3BP):​c.4163-268G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,994 control chromosomes in the GnomAD database, including 4,370 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 0.23 (4370 hom., cov: 32)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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.4163-268G>T		intron	N/A	NP_001362476.1	D3YTG3
	ABI3BP	NM_001375550.1		c.4121-268G>T		intron	N/A	NP_001362479.1
	ABI3BP	NM_001375549.2		c.4115-268G>T		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.4163-268G>T		intron	N/A	ENSP00000420524.2	D3YTG3
	ABI3BP	ENST00000284322.10	TSL:1	c.2009-268G>T		intron	N/A	ENSP00000284322.6	Q7Z7G0-1
	ABI3BP	ENST00000470336.5	TSL:1	n.626-268G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34872 AN: 151876 Hom.: 4370 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.230 AC: 34900 AN: 151994 Hom.: 4370 Cov.: 32 AF XY: 0.233 AC XY: 17299 AN XY: 74278

African (AFR) AF: 0.316 AC: 13082 AN: 41436

American (AMR) AF: 0.215 AC: 3287 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 762 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1651 AN: 5160

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4816

European-Finnish (FIN) AF: 0.202 AC: 2134 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12118 AN: 67962

Other (OTH) AF: 0.216 AC: 455 AN: 2110

Alfa AF: 0.196 Hom.: 3875

Bravo AF: 0.237

Asia WGS AF: 0.235 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.42
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: rs7613610; hg19: chr3-100499321; COSMIC: COSV52533106; COSMIC: COSV52533106;