rs4546368

Positions:

• chr5-149159537-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM3	NM_014945.5	c.13+17429C>T		intron_variant		ENST00000309868.12	NP_055760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM3	ENST00000309868.12	c.13+17429C>T		intron_variant		1	NM_014945.5	ENSP00000310309	P1

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

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.545

Alfa AF: 0.556 Hom.: 36821

Bravo AF: 0.544

Asia WGS AF: 0.558 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.80

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

Other links and lift over

dbSNP: rs4546368; hg19: chr5-148539100; COSMIC: COSV58640668; COSMIC: COSV58640668;