NM_002313.7:c.1120-343A>G

Variant names:

• chr10-114473475-T-C
• rs1535386
• NM_002313.7:c.1120-343A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002313.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	NM_002313.7	MANE Select	c.1120-343A>G		intron	N/A	NP_002304.3
	ABLIM1	NM_001322882.2		c.1024-343A>G		intron	N/A	NP_001309811.1	O14639-6
	ABLIM1	NM_001003407.2		c.940-343A>G		intron	N/A	NP_001003407.1	O14639-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	ENST00000533213.7	TSL:5 MANE Select	c.1120-343A>G		intron	N/A	ENSP00000433629.3	O14639-1
	ABLIM1	ENST00000649363.1		c.1168-343A>G		intron	N/A	ENSP00000497150.1	A0A3B3IS55
	ABLIM1	ENST00000369256.6	TSL:5	c.1024-343A>G		intron	N/A	ENSP00000358260.3	O14639-6

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

African (AFR) AF: 0.184 AC: 7620 AN: 41508

American (AMR) AF: 0.414 AC: 6317 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2143 AN: 5178

South Asian (SAS) AF: 0.471 AC: 2267 AN: 4818

European-Finnish (FIN) AF: 0.419 AC: 4416 AN: 10548

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31696 AN: 67966

Other (OTH) AF: 0.404 AC: 853 AN: 2112

Alfa AF: 0.448 Hom.: 36167

Bravo AF: 0.370

Asia WGS AF: 0.407 AC: 1410 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.9
DANN	Benign	0.89
PhyloP100		0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1535386; hg19: chr10-116233234;