rs16841542

Variant names:

• chr4-8000664-T-G
• rs16841542
• NM_001130083.2:c.1618+7395A>C

Variant summary

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

The NM_001130083.2(ABLIM2):​c.1618+7395A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,982 control chromosomes in the GnomAD database, including 2,295 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 0.15 (2295 hom., cov: 32)
• Consequence: ABLIM2 NM_001130083.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130083.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM2	NM_001130083.2	MANE Select	c.1618+7395A>C		intron	N/A	NP_001123555.1
	ABLIM2	NM_001130084.2		c.1516+7395A>C		intron	N/A	NP_001123556.1
	ABLIM2	NM_001130085.2		c.1516+7395A>C		intron	N/A	NP_001123557.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM2	ENST00000447017.7	TSL:1 MANE Select	c.1618+7395A>C		intron	N/A	ENSP00000393511.2
	ABLIM2	ENST00000341937.9	TSL:1	c.1516+7395A>C		intron	N/A	ENSP00000342813.5
	ABLIM2	ENST00000361581.9	TSL:1	c.1516+7395A>C		intron	N/A	ENSP00000355003.5

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22779 AN: 151864 Hom.: 2279 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.150 AC: 22828 AN: 151982 Hom.: 2295 Cov.: 32 AF XY: 0.148 AC XY: 10967 AN XY: 74308

African (AFR) AF: 0.279 AC: 11530 AN: 41368

American (AMR) AF: 0.116 AC: 1771 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.0711 AC: 366 AN: 5150

South Asian (SAS) AF: 0.0709 AC: 342 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6834 AN: 67996

Other (OTH) AF: 0.137 AC: 287 AN: 2102

Alfa AF: 0.112 Hom.: 660

Bravo AF: 0.155

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.41
PhyloP100		-1.1
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: rs16841542; hg19: chr4-8002391;