chr10-114554076-A-G

Variant names:

• chr10-114554076-A-G
• rs2483535
• NM_002313.7:c.674-6300T>C

Variant summary

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

The NM_002313.7(ABLIM1):​c.674-6300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,068 control chromosomes in the GnomAD database, including 13,856 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 0.37 (13856 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.674-6300T>C		intron_variant	Intron 4 of 22	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.674-6300T>C		intron_variant	Intron 4 of 22	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56393 AN: 151950 Hom.: 13808 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.372 AC: 56501 AN: 152068 Hom.: 13856 Cov.: 32 AF XY: 0.367 AC XY: 27257 AN XY: 74344

African (AFR) AF: 0.698 AC: 28956 AN: 41460

American (AMR) AF: 0.371 AC: 5675 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1900 AN: 5160

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1854 AN: 10588

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14778 AN: 67970

Other (OTH) AF: 0.354 AC: 749 AN: 2114

Alfa AF: 0.307 Hom.: 1770

Bravo AF: 0.403

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.73
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2483535; hg19: chr10-116313835;