4-8109055-C-T

Variant names:

• chr4-8109055-C-T
• rs1878519
• NM_001130083.2:c.11-2418G>A

Variant summary

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

The NM_001130083.2(ABLIM2):​c.11-2418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,142 control chromosomes in the GnomAD database, including 13,318 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 0.42 (13318 hom., cov: 34)
• Consequence: ABLIM2 NM_001130083.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 1 publications found

Genes affected

ABLIM2 (HGNC:19195): (actin binding LIM protein family member 2) Predicted to enable actin filament binding activity. Predicted to be involved in lamellipodium assembly. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in actin cytoskeleton. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM2	NM_001130083.2	c.11-2418G>A		intron_variant	Intron 1 of 20	ENST00000447017.7	NP_001123555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM2	ENST00000447017.7	c.11-2418G>A		intron_variant	Intron 1 of 20	1	NM_001130083.2	ENSP00000393511.2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63207 AN: 152024 Hom.: 13321 Cov.: 34

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.416 AC: 63221 AN: 152142 Hom.: 13318 Cov.: 34 AF XY: 0.415 AC XY: 30884 AN XY: 74370

African (AFR) AF: 0.345 AC: 14321 AN: 41502

American (AMR) AF: 0.387 AC: 5923 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1552 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1976 AN: 5164

South Asian (SAS) AF: 0.521 AC: 2513 AN: 4820

European-Finnish (FIN) AF: 0.419 AC: 4435 AN: 10594

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31204 AN: 67978

Other (OTH) AF: 0.435 AC: 920 AN: 2114

Alfa AF: 0.449 Hom.: 26369

Bravo AF: 0.407

Asia WGS AF: 0.424 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.36
PhyloP100		-0.70
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: rs1878519; hg19: chr4-8110782;