rs9512

Positions:

• chr5-149260199-G-A
• chr5-149260199-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309868.12(ABLIM3):​c.*1795G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,690 control chromosomes in the GnomAD database, including 20,722 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 0.51 (20621 hom., cov: 30)
  • Exomes 𝑓: 0.48 (101 hom.)
• Consequence: ABLIM3 ENST00000309868.12 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM3	NM_014945.5	c.*1795G>A		3_prime_UTR_variant	24/24	ENST00000309868.12	NP_055760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM3	ENST00000309868.12	c.*1795G>A		3_prime_UTR_variant	24/24	1	NM_014945.5	ENSP00000310309	P1
	ENST00000522685.1	n.87+16491C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000523176.1	n.116+16491C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77840 AN: 151730 Hom.: 20593 Cov.: 30

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.469

GnomAD4 exome AF: 0.482 AC: 405 AN: 840 Hom.: 101 Cov.: 0 AF XY: 0.494 AC XY: 235 AN XY: 476

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.381

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.422

Gnomad4 NFE exome AF: 0.557

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.513 AC: 77915 AN: 151850 Hom.: 20621 Cov.: 30 AF XY: 0.503 AC XY: 37325 AN XY: 74210

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.471

Alfa AF: 0.492 Hom.: 7183

Bravo AF: 0.520

Asia WGS AF: 0.542 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.37
DANN	Benign	0.68

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: rs9512; hg19: chr5-148639762; COSMIC: COSV58641405; COSMIC: COSV58641405;