rs12570718

Variant names:

• chr10-114657200-C-T
• rs12570718
• NM_002313.7:c.244+757G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000305445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.244+757G>A		intron_variant	Intron 1 of 22	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.244+757G>A		intron_variant	Intron 1 of 22	5	NM_002313.7	ENSP00000433629.3

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

African (AFR) AF: 0.135 AC: 5616 AN: 41514

American (AMR) AF: 0.346 AC: 5287 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.189 AC: 977 AN: 5164

South Asian (SAS) AF: 0.411 AC: 1983 AN: 4824

European-Finnish (FIN) AF: 0.336 AC: 3551 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28352 AN: 67946

Other (OTH) AF: 0.324 AC: 685 AN: 2116

Alfa AF: 0.383 Hom.: 50323

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
PhyloP100		-0.81
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: rs12570718; hg19: chr10-116416959;