rs217190

chr10-114701663-A-G

Variant summary

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

The NM_001322884.3(ABLIM1):c.13+66398T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,130 control chromosomes in the GnomAD database, including 5,559 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 0.22 (5559 hom., cov: 32)
• Consequence: ABLIM1 NM_001322884.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABLIM1	NM_001322884.3	c.13+66398T>C		intron_variant
ABLIM1	NM_001322885.3	c.13+66398T>C		intron_variant
ABLIM1	NM_001322886.3	c.13+66398T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABLIM1	ENST00000651092.1	c.-213+66398T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33800 AN: 152012 Hom.: 5547 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.00654

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.222 AC: 33840 AN: 152130 Hom.: 5559 Cov.: 32 AF XY: 0.217 AC XY: 16166 AN XY: 74384

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.00655

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.216

Alfa AF: 0.142 Hom.: 3009

Bravo AF: 0.238

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.52
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs217190; hg19: chr10-116461422;