rs808338

Variant names:

• chr10-114734785-T-C
• rs808338
• NM_001322884.3:c.13+33276A>G

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+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
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	NM_001322884.3		c.13+33276A>G		intron	N/A	NP_001309813.1
	ABLIM1	NM_001322885.3		c.13+33276A>G		intron	N/A	NP_001309814.1
	ABLIM1	NM_001322886.3		c.13+33276A>G		intron	N/A	NP_001309815.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	ENST00000651092.1		c.-213+33276A>G		intron	N/A	ENSP00000499163.1

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

African (AFR) AF: 0.0179 AC: 745 AN: 41516

American (AMR) AF: 0.0660 AC: 1009 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5186

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1435 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7095 AN: 67996

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.0928 Hom.: 342

Bravo AF: 0.0662

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs808338; hg19: chr10-116494544;