chr5-149159537-C-T

Variant names:

• chr5-149159537-C-T
• rs4546368
• NM_014945.5:c.13+17429C>T

Variant summary

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

The NM_014945.5(ABLIM3):​c.13+17429C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,916 control chromosomes in the GnomAD database, including 22,479 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 0.54 (22479 hom., cov: 31)
• Consequence: ABLIM3 NM_014945.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.658 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.13+17429C>T		intron	N/A	NP_055760.1
	ABLIM3	NM_001301015.3		c.13+17429C>T		intron	N/A	NP_001287944.1
	ABLIM3	NM_001301018.3		c.13+17429C>T		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.13+17429C>T		intron	N/A	ENSP00000310309.7
	ABLIM3	ENST00000506113.5	TSL:1	c.13+17429C>T		intron	N/A	ENSP00000425394.1
	ABLIM3	ENST00000508983.5	TSL:1	c.13+17429C>T		intron	N/A	ENSP00000420855.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81792 AN: 151798 Hom.: 22473 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.539 AC: 81832 AN: 151916 Hom.: 22479 Cov.: 31 AF XY: 0.543 AC XY: 40324 AN XY: 74246

African (AFR) AF: 0.452 AC: 18728 AN: 41390

American (AMR) AF: 0.668 AC: 10214 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3167 AN: 5160

South Asian (SAS) AF: 0.411 AC: 1981 AN: 4818

European-Finnish (FIN) AF: 0.619 AC: 6515 AN: 10526

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37735 AN: 67956

Other (OTH) AF: 0.545 AC: 1150 AN: 2110

Alfa AF: 0.551 Hom.: 61736

Bravo AF: 0.544

Asia WGS AF: 0.558 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.48
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: rs4546368; hg19: chr5-148539100; COSMIC: COSV58640668; COSMIC: COSV58640668;