chr10-114575487-G-A

Position:

• chr10-114575487-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_002313.7(ABLIM1):​c.492C>T​(p.Phe164Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,613,882 control chromosomes in the GnomAD database, including 36,147 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 0.26 (6375 hom., cov: 32)
  • Exomes 𝑓: 0.19 (29772 hom.)
• Consequence: ABLIM1 NM_002313.7 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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]

ABLIM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BP7: Synonymous conserved (PhyloP=0.308 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.492C>T	p.Phe164Phe	synonymous_variant	3/23	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.492C>T	p.Phe164Phe	synonymous_variant	3/23	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40069 AN: 151924 Hom.: 6361 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.280

GnomAD3 exomes AF: 0.218 AC: 54733 AN: 251250 Hom.: 6738 AF XY: 0.208 AC XY: 28302 AN XY: 135776

Gnomad AFR exome AF: 0.438

Gnomad AMR exome AF: 0.314

Gnomad ASJ exome AF: 0.233

Gnomad EAS exome AF: 0.231

Gnomad SAS exome AF: 0.186

Gnomad FIN exome AF: 0.115

Gnomad NFE exome AF: 0.181

Gnomad OTH exome AF: 0.228

GnomAD4 exome AF: 0.194 AC: 283517 AN: 1461840 Hom.: 29772 Cov.: 33 AF XY: 0.193 AC XY: 140029 AN XY: 727228

Gnomad4 AFR exome AF: 0.448

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.238

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.215

GnomAD4 genome AF: 0.264 AC: 40136 AN: 152042 Hom.: 6375 Cov.: 32 AF XY: 0.261 AC XY: 19426 AN XY: 74322

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.276

Alfa AF: 0.202 Hom.: 6766

Bravo AF: 0.288

Asia WGS AF: 0.224 AC: 777 AN: 3478

EpiCase AF: 0.198

EpiControl AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	8.8
DANN	Benign	0.78

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: rs985273; hg19: chr10-116335246; COSMIC: COSV53302556;