chr10-114567791-T-C

Variant names:

• chr10-114567791-T-C
• rs10885582
• NM_002313.7:c.673+3506A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002313.7(ABLIM1):​c.673+3506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,126 control chromosomes in the GnomAD database, including 12,974 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 0.38 (12974 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 13 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002313.7. 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_002313.7	MANE Select	c.673+3506A>G		intron	N/A	NP_002304.3
	ABLIM1	NM_001322882.2		c.493+3506A>G		intron	N/A	NP_001309811.1
	ABLIM1	NM_001003407.2		c.493+3506A>G		intron	N/A	NP_001003407.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	ENST00000533213.7	TSL:5 MANE Select	c.673+3506A>G		intron	N/A	ENSP00000433629.3
	ABLIM1	ENST00000649363.1		c.673+3506A>G		intron	N/A	ENSP00000497150.1
	ABLIM1	ENST00000369256.6	TSL:5	c.493+3506A>G		intron	N/A	ENSP00000358260.3

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57995 AN: 152008 Hom.: 12973 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.381 AC: 57997 AN: 152126 Hom.: 12974 Cov.: 32 AF XY: 0.380 AC XY: 28278 AN XY: 74360

African (AFR) AF: 0.167 AC: 6912 AN: 41510

American (AMR) AF: 0.352 AC: 5381 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1637 AN: 3472

East Asian (EAS) AF: 0.110 AC: 567 AN: 5178

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4818

European-Finnish (FIN) AF: 0.530 AC: 5599 AN: 10566

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34418 AN: 67988

Other (OTH) AF: 0.397 AC: 837 AN: 2106

Alfa AF: 0.461 Hom.: 47876

Bravo AF: 0.357

Asia WGS AF: 0.282 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10885582; hg19: chr10-116327550;