5-149227193-A-G

Variant names:

• chr5-149227193-A-G
• rs2918268
• NM_014945.5:c.758-3456A>G

Variant summary

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

The NM_014945.5(ABLIM3):​c.758-3456A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,974 control chromosomes in the GnomAD database, including 19,406 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 0.50 (19406 hom., cov: 31)
• Consequence: ABLIM3 NM_014945.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014945.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM3	NM_014945.5	MANE Select	c.758-3456A>G		intron	N/A	NP_055760.1
	ABLIM3	NM_001301015.3		c.758-3456A>G		intron	N/A	NP_001287944.1
	ABLIM3	NM_001301018.3		c.758-3456A>G		intron	N/A	NP_001287947.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM3	ENST00000309868.12	TSL:1 MANE Select	c.758-3456A>G		intron	N/A	ENSP00000310309.7
	ABLIM3	ENST00000506113.5	TSL:1	c.758-3456A>G		intron	N/A	ENSP00000425394.1
	ABLIM3	ENST00000508983.5	TSL:1	c.758-3456A>G		intron	N/A	ENSP00000420855.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75390 AN: 151856 Hom.: 19380 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.497 AC: 75460 AN: 151974 Hom.: 19406 Cov.: 31 AF XY: 0.487 AC XY: 36210 AN XY: 74284

African (AFR) AF: 0.615 AC: 25474 AN: 41422

American (AMR) AF: 0.415 AC: 6338 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3201 AN: 5160

South Asian (SAS) AF: 0.470 AC: 2260 AN: 4810

European-Finnish (FIN) AF: 0.370 AC: 3911 AN: 10566

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31660 AN: 67972

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.443 Hom.: 7947

Bravo AF: 0.506

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.55
PhyloP100		0.22
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: rs2918268; hg19: chr5-148606756; COSMIC: COSV58640966;