rs703349

Positions:

• chr10-114759762-C-T

Variant summary

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

The NM_001322884.3(ABLIM1):​c.13+8299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,008 control chromosomes in the GnomAD database, including 37,812 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 0.70 (37812 hom., cov: 31)
• Consequence: ABLIM1 NM_001322884.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABLIM1	NM_001322884.3	c.13+8299G>A		intron_variant			NP_001309813.1
ABLIM1	NM_001322885.3	c.13+8299G>A		intron_variant			NP_001309814.1
ABLIM1	NM_001322886.3	c.13+8299G>A		intron_variant			NP_001309815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000651092.1	c.-213+8299G>A		intron_variant				ENSP00000499163.1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106932 AN: 151890 Hom.: 37778 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.704 AC: 107033 AN: 152008 Hom.: 37812 Cov.: 31 AF XY: 0.703 AC XY: 52247 AN XY: 74274

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.698

Alfa AF: 0.721 Hom.: 18037

Bravo AF: 0.701

Asia WGS AF: 0.622 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703349; hg19: chr10-116519521;