10-114473475-T-C

Position:

• chr10-114473475-T-C

Variant summary

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

The NM_002313.7(ABLIM1):​c.1120-343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,072 control chromosomes in the GnomAD database, including 11,960 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 0.38 (11960 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712

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=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.1120-343A>G		intron_variant		ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.1120-343A>G		intron_variant		5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57490 AN: 151954 Hom.: 11960 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.378 AC: 57491 AN: 152072 Hom.: 11960 Cov.: 32 AF XY: 0.379 AC XY: 28178 AN XY: 74334

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.404

Alfa AF: 0.456 Hom.: 24180

Bravo AF: 0.370

Asia WGS AF: 0.407 AC: 1410 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.9
DANN	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1535386; hg19: chr10-116233234;