rs703349

Variant names:

• chr10-114759762-C-T
• rs703349
• NM_001322884.3:c.13+8299G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322884.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	NM_001322884.3		c.13+8299G>A		intron	N/A	NP_001309813.1
	ABLIM1	NM_001322885.3		c.13+8299G>A		intron	N/A	NP_001309814.1
	ABLIM1	NM_001322886.3		c.13+8299G>A		intron	N/A	NP_001309815.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	ENST00000651092.1		c.-213+8299G>A		intron	N/A	ENSP00000499163.1	A0A494C1P1

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

African (AFR) AF: 0.694 AC: 28789 AN: 41464

American (AMR) AF: 0.658 AC: 10050 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2595 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2566 AN: 5162

South Asian (SAS) AF: 0.685 AC: 3288 AN: 4802

European-Finnish (FIN) AF: 0.755 AC: 7974 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49339 AN: 67966

Other (OTH) AF: 0.698 AC: 1473 AN: 2110

Alfa AF: 0.721 Hom.: 20088

Bravo AF: 0.701

Asia WGS AF: 0.622 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs703349; hg19: chr10-116519521;