5-149260199-G-T

Variant names:

• chr5-149260199-G-T
• rs9512
• NM_014945.5:c.*1795G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014945.5(ABLIM3):​c.*1795G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ABLIM3 NM_014945.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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.*1795G>T		3_prime_UTR	Exon 24 of 24	NP_055760.1
	ABLIM3	NM_001301015.3		c.*1795G>T		3_prime_UTR	Exon 23 of 23	NP_001287944.1
	ABLIM3	NM_001301018.3		c.*1795G>T		3_prime_UTR	Exon 23 of 23	NP_001287947.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM3	ENST00000309868.12	TSL:1 MANE Select	c.*1795G>T		3_prime_UTR	Exon 24 of 24	ENSP00000310309.7
	ABLIM3	ENST00000506113.5	TSL:1	c.*1795G>T		3_prime_UTR	Exon 23 of 23	ENSP00000425394.1
	ABLIM3	ENST00000504238.5	TSL:1	c.*624G>T		3_prime_UTR	Exon 19 of 19	ENSP00000421183.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.30
DANN	Benign	0.75
PhyloP100		-0.32

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: rs9512; hg19: chr5-148639762;