rs808338

chr10-114734785-T-C

Variant summary

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

The NM_001322884.3(ABLIM1):c.13+33276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,168 control chromosomes in the GnomAD database, including 551 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 0.074 (551 hom., cov: 32)
• Consequence: ABLIM1 NM_001322884.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABLIM1	NM_001322884.3	c.13+33276A>G		intron_variant
ABLIM1	NM_001322885.3	c.13+33276A>G		intron_variant
ABLIM1	NM_001322886.3	c.13+33276A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABLIM1	ENST00000651092.1	c.-213+33276A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11340 AN: 152050 Hom.: 552 Cov.: 32

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0745 AC: 11331 AN: 152168 Hom.: 551 Cov.: 32 AF XY: 0.0755 AC XY: 5618 AN XY: 74402

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.0660

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0931 Hom.: 317

Bravo AF: 0.0662

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.6
Dann	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs808338; hg19: chr10-116494544;