chr3-100777836-C-G

Variant names:

• chr3-100777836-C-G
• rs9873555
• NM_001375547.2:c.4333+448G>C

Variant summary

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

The NM_001375547.2(ABI3BP):​c.4333+448G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,156 control chromosomes in the GnomAD database, including 1,443 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 0.13 (1443 hom., cov: 32)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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.4333+448G>C		intron	N/A	NP_001362476.1	D3YTG3
	ABI3BP	NM_001375550.1		c.4291+448G>C		intron	N/A	NP_001362479.1
	ABI3BP	NM_001375549.2		c.4285+448G>C		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.4333+448G>C		intron	N/A	ENSP00000420524.2	D3YTG3
	ABI3BP	ENST00000284322.10	TSL:1	c.2179+448G>C		intron	N/A	ENSP00000284322.6	Q7Z7G0-1
	ABI3BP	ENST00000470336.5	TSL:1	n.796+448G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20254 AN: 152038 Hom.: 1443 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.133 AC: 20258 AN: 152156 Hom.: 1443 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74392

African (AFR) AF: 0.130 AC: 5375 AN: 41504

American (AMR) AF: 0.112 AC: 1710 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0636 AC: 307 AN: 4826

European-Finnish (FIN) AF: 0.108 AC: 1141 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10654 AN: 67988

Other (OTH) AF: 0.139 AC: 294 AN: 2114

Alfa AF: 0.138 Hom.: 196

Bravo AF: 0.135

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.96
DANN	Benign	0.68
PhyloP100		-1.4
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: rs9873555; hg19: chr3-100496680;