rs7613610

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.420
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ABI3BPNM_001375547.2 linkuse as main transcriptc.4163-268G>T intron_variant ENST00000471714.6 NP_001362476.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ABI3BPENST00000471714.6 linkuse as main transcriptc.4163-268G>T intron_variant 5 NM_001375547.2 ENSP00000420524 A2

Frequencies

GnomAD3 genomes
AF:
0.230
AC:
34872
AN:
151876
Hom.:
4370
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.316
Gnomad4 AMR
AF:
0.215
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.320
Gnomad4 SAS
AF:
0.218
Gnomad4 FIN
AF:
0.202
Gnomad4 NFE
AF:
0.178
Gnomad4 OTH
AF:
0.216
Alfa
AF:
0.191
Hom.:
2719
Bravo
AF:
0.237
Asia WGS
AF:
0.235
AC:
815
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
11
DANN
Benign
0.62

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7613610; hg19: chr3-100499321; COSMIC: COSV52533106; COSMIC: COSV52533106; API