rs12570718

chr10-114657200-C-T

Variant summary

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

The NM_002313.7(ABLIM1):c.244+757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,096 control chromosomes in the GnomAD database, including 8,668 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 0.32 (8668 hom., cov: 33)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

ABLIM1 (HGNC:78): (actin binding LIM protein 1) This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABLIM1	NM_002313.7	c.244+757G>A		intron_variant		ENST00000533213.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABLIM1	ENST00000533213.7	c.244+757G>A		intron_variant		5	NM_002313.7	A2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48059 AN: 151978 Hom.: 8656 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.316 AC: 48087 AN: 152096 Hom.: 8668 Cov.: 33 AF XY: 0.314 AC XY: 23375 AN XY: 74348

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.324

Alfa AF: 0.393 Hom.: 25474

Bravo AF: 0.305

Asia WGS AF: 0.297 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.5
Dann	Benign	0.72

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: rs12570718; hg19: chr10-116416959;