rs2483535

chr10-114554076-A-G

Variant summary

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

The NM_002313.7(ABLIM1):c.674-6300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,068 control chromosomes in the GnomAD database, including 13,856 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 0.37 (13856 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABLIM1	NM_002313.7	c.674-6300T>C		intron_variant		ENST00000533213.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABLIM1	ENST00000533213.7	c.674-6300T>C		intron_variant		5	NM_002313.7	A2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56393 AN: 151950 Hom.: 13808 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.372 AC: 56501 AN: 152068 Hom.: 13856 Cov.: 32 AF XY: 0.367 AC XY: 27257 AN XY: 74344

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.354

Alfa AF: 0.295 Hom.: 1577

Bravo AF: 0.403

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.3
Dann	Benign	0.73

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: rs2483535; hg19: chr10-116313835;