rs9850273

Variant names:

• chr3-100780521-G-A
• rs9850273
• NM_001375547.2:c.4163-312C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-100780521-G-A
• chr3-100780521-G-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.4163-312C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,738 control chromosomes in the GnomAD database, including 9,714 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 0.31 (9714 hom., cov: 32)
• Consequence: ABI3BP NM_001375547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABI3BP	NM_001375547.2	c.4163-312C>T		intron_variant	Intron 57 of 67	ENST00000471714.6	NP_001362476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABI3BP	ENST00000471714.6	c.4163-312C>T		intron_variant	Intron 57 of 67	5	NM_001375547.2	ENSP00000420524.2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46849 AN: 151620 Hom.: 9688 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.309 AC: 46925 AN: 151738 Hom.: 9714 Cov.: 32 AF XY: 0.310 AC XY: 22960 AN XY: 74132

African (AFR) AF: 0.590 AC: 24389 AN: 41342

American (AMR) AF: 0.246 AC: 3743 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 851 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1588 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4808

European-Finnish (FIN) AF: 0.203 AC: 2132 AN: 10514

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12215 AN: 67904

Other (OTH) AF: 0.271 AC: 571 AN: 2106

Alfa AF: 0.249 Hom.: 1024

Bravo AF: 0.328

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		0.056
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: rs9850273; hg19: chr3-100499365;