4-8069066-T-G

Variant names:

• chr4-8069066-T-G
• rs6829649
• NM_001130083.2:c.676-8012A>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.676-8012A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,176 control chromosomes in the GnomAD database, including 1,975 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 (1975 hom., cov: 33)
• Consequence: ABLIM2 NM_001130083.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM2	NM_001130083.2	c.676-8012A>C		intron_variant	Intron 6 of 20	ENST00000447017.7	NP_001123555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM2	ENST00000447017.7	c.676-8012A>C		intron_variant	Intron 6 of 20	1	NM_001130083.2	ENSP00000393511.2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23292 AN: 152058 Hom.: 1972 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.153 AC: 23304 AN: 152176 Hom.: 1975 Cov.: 33 AF XY: 0.153 AC XY: 11392 AN XY: 74416

African (AFR) AF: 0.216 AC: 8984 AN: 41528

American (AMR) AF: 0.105 AC: 1611 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3466

East Asian (EAS) AF: 0.148 AC: 765 AN: 5158

South Asian (SAS) AF: 0.187 AC: 901 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8789 AN: 68004

Other (OTH) AF: 0.152 AC: 321 AN: 2116

Alfa AF: 0.129 Hom.: 2746

Bravo AF: 0.150

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		0.44
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: rs6829649; hg19: chr4-8070793;