rs11939078

chr4-8005201-C-T

Variant summary

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

The NM_001130083.2(ABLIM2):c.1618+2858G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 437,630 control chromosomes in the GnomAD database, including 15,443 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 0.25 (5076 hom., cov: 33)
  • Exomes 𝑓: 0.26 (10367 hom.)
• Consequence: ABLIM2 NM_001130083.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

ABLIM2 (HGNC:19195): (actin binding LIM protein family member 2) Predicted to enable actin filament binding activity. Predicted to be involved in lamellipodium assembly. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABLIM2	NM_001130083.2	c.1618+2858G>A		intron_variant		ENST00000447017.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABLIM2	ENST00000447017.7	c.1618+2858G>A		intron_variant		1	NM_001130083.2	P4

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38094 AN: 152118 Hom.: 5080 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.250

GnomAD4 exome AF: 0.264 AC: 75219 AN: 285394 Hom.: 10367 AF XY: 0.261 AC XY: 41277 AN XY: 158034

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.334

Gnomad4 EAS exome AF: 0.239

Gnomad4 SAS exome AF: 0.231

Gnomad4 FIN exome AF: 0.240

Gnomad4 NFE exome AF: 0.305

Gnomad4 OTH exome AF: 0.270

GnomAD4 genome AF: 0.250 AC: 38085 AN: 152236 Hom.: 5076 Cov.: 33 AF XY: 0.244 AC XY: 18137 AN XY: 74436

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.248

Alfa AF: 0.288 Hom.: 1105

Bravo AF: 0.244

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.7
Dann	Benign	0.82

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: rs11939078; hg19: chr4-8006928; COSMIC: COSV56403353; COSMIC: COSV56403353;