rs7136648

chr12-50231039-G-Achr12-50231039-G-Cchr12-50231039-G-T

Variant summary

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

The NM_016357.5(LIMA1):c.165+626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,084 control chromosomes in the GnomAD database, including 34,700 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 0.66 (34700 hom., cov: 33)
• Consequence: LIMA1 NM_016357.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

Genes affected

LIMA1 (HGNC:24636): (LIM domain and actin binding 1) This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIMA1	NM_016357.5	c.165+626C>T		intron_variant		ENST00000341247.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIMA1	ENST00000341247.9	c.165+626C>T		intron_variant		1	NM_016357.5	A2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99634 AN: 151968 Hom.: 34650 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.656 AC: 99734 AN: 152084 Hom.: 34700 Cov.: 33 AF XY: 0.659 AC XY: 48963 AN XY: 74334

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.639

Alfa AF: 0.555 Hom.: 3509

Bravo AF: 0.674

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	16
Dann	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs7136648; hg19: chr12-50624822;