rs4751909

Variant names:

• chr10-114442684-G-A
• rs4751909
• NM_002313.7:c.1934-898C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002313.7(ABLIM1):​c.1934-898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,988 control chromosomes in the GnomAD database, including 12,272 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 0.40 (12272 hom., cov: 33)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.1934-898C>T		intron_variant	Intron 17 of 22	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.1934-898C>T		intron_variant	Intron 17 of 22	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61271 AN: 151870 Hom.: 12263 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.403 AC: 61322 AN: 151988 Hom.: 12272 Cov.: 33 AF XY: 0.404 AC XY: 30029 AN XY: 74296

African (AFR) AF: 0.378 AC: 15651 AN: 41418

American (AMR) AF: 0.409 AC: 6247 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2133 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4337 AN: 10538

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28069 AN: 67982

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.409 Hom.: 2196

Bravo AF: 0.396

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		0.35
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: rs4751909; hg19: chr10-116202443;