10-114605557-C-T

Position:

• chr10-114605557-C-T

Variant summary

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

The NM_002313.7(ABLIM1):​c.245-3596G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,098 control chromosomes in the GnomAD database, including 52,291 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 0.82 (52291 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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]

ABLIM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.245-3596G>A		intron_variant		ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.245-3596G>A		intron_variant		5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124479 AN: 151978 Hom.: 52258 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.819 AC: 124567 AN: 152098 Hom.: 52291 Cov.: 32 AF XY: 0.824 AC XY: 61259 AN XY: 74366

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.816

Alfa AF: 0.873 Hom.: 60317

Bravo AF: 0.806

Asia WGS AF: 0.952 AC: 3307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.44

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: rs2483589; hg19: chr10-116365316;