5-149239835-G-T

Variant names:

• chr5-149239835-G-T
• rs552321551
• NM_014945.5:c.1151G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_014945.5(ABLIM3):​c.1151G>T​(p.Arg384Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,458,506 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R384Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: ABLIM3 NM_014945.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.55
• Publications: 0 publications found

Genes affected

ABLIM3 (HGNC:29132): (actin binding LIM protein family member 3) This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]

ENSG00000253406 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM3	NM_014945.5	c.1151G>T	p.Arg384Leu	missense_variant	Exon 13 of 24	ENST00000309868.12	NP_055760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM3	ENST00000309868.12	c.1151G>T	p.Arg384Leu	missense_variant	Exon 13 of 24	1	NM_014945.5	ENSP00000310309.7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458506 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 725482

African (AFR) AF: 0.00 AC: 0 AN: 33274

American (AMR) AF: 0.00 AC: 0 AN: 44372

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26014

East Asian (EAS) AF: 0.00 AC: 0 AN: 39182

South Asian (SAS) AF: 0.0000117 AC: 1 AN: 85828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53384

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5764

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1110422

Other (OTH) AF: 0.00 AC: 0 AN: 60266

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.55
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	.;T;T;.;.
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.98	D;.;D;D;D
M_CAP	Benign	0.039	D
MetaRNN	Uncertain	0.62	D;D;D;D;D
MetaSVM	Benign	-0.92	T
MutationAssessor	Uncertain	2.9	.;M;M;.;.
PhyloP100		6.5
PrimateAI	Uncertain	0.65	T
PROVEAN	Uncertain	-2.8	D;D;D;D;D
REVEL	Benign	0.26
Sift	Uncertain	0.0020	D;D;D;D;D
Sift4G	Uncertain	0.026	D;D;D;D;D
Polyphen		0.12	B;P;P;B;.
Vest4		0.82
MutPred		0.29		.;Loss of MoRF binding (P = 0.0806);Loss of MoRF binding (P = 0.0806);.;Loss of MoRF binding (P = 0.0806);
MVP		0.63
MPC		0.36
ClinPred		0.96	D
GERP RS		4.1
Varity_R		0.34
gMVP		0.72
Mutation Taster		=54/46	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs552321551; hg19: chr5-148619398;