rs78022502

chr2-127638592-A-C

Variant summary

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

The NM_001161403.3(LIMS2):c.*689T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,812 control chromosomes in the GnomAD database, including 268 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 0.055 (264 hom., cov: 33)
  • Exomes 𝑓: 0.058 (4 hom.)
• Consequence: LIMS2 NM_001161403.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

Genes affected

LIMS2 (HGNC:16084): (LIM zinc finger domain containing 2) This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIMS2	NM_001161403.3	c.*689T>G		3_prime_UTR_variant	10/10	ENST00000355119.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIMS2	ENST00000355119.9	c.*689T>G		3_prime_UTR_variant	10/10	1	NM_001161403.3	P1

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8442 AN: 152162 Hom.: 265 Cov.: 33

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00952

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0574

GnomAD4 exome AF: 0.0583 AC: 31 AN: 532 Hom.: 4 Cov.: 0 AF XY: 0.0562 AC XY: 19 AN XY: 338

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0556

Gnomad4 FIN exome AF: 0.0180

Gnomad4 NFE exome AF: 0.0923

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0555 AC: 8450 AN: 152280 Hom.: 264 Cov.: 33 AF XY: 0.0536 AC XY: 3989 AN XY: 74460

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0644

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00973

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0566 Hom.: 42

Bravo AF: 0.0590

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.33

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: rs78022502; hg19: chr2-128396167; COSMIC: COSV61442806; COSMIC: COSV61442806;