rs4141404

Variant names:

• chr22-31279199-A-C
• rs4141404
• NM_005569.4:c.*758A>C

Your query was ambiguous. Multiple possible variants found:

• chr22-31279199-A-C
• chr22-31279199-A-G
• chr22-31279199-A-T

Variant summary

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

The NM_005569.4(LIMK2):​c.*758A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,248 control chromosomes in the GnomAD database, including 48,685 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 0.79 (48673 hom., cov: 33)
  • Exomes 𝑓: 0.75 (12 hom.)
• Consequence: LIMK2 NM_005569.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 37 publications found

Genes affected

LIMK2 (HGNC:6614): (LIM domain kinase 2) There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. The protein encoded by this gene is phosphorylated and activated by ROCK, a downstream effector of Rho, and the encoded protein, in turn, phosphorylates cofilin, inhibiting its actin-depolymerizing activity. It is thought that this pathway contributes to Rho-induced reorganization of the actin cytoskeleton. At least three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005569.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIMK2	NM_005569.4	MANE Select	c.*758A>C		3_prime_UTR	Exon 16 of 16	NP_005560.1
	LIMK2	NM_016733.3		c.*758A>C		3_prime_UTR	Exon 15 of 15	NP_057952.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIMK2	ENST00000331728.9	TSL:1 MANE Select	c.*758A>C		3_prime_UTR	Exon 16 of 16	ENSP00000332687.4
	LIMK2	ENST00000333611.8	TSL:1	c.*758A>C		3_prime_UTR	Exon 15 of 15	ENSP00000330470.4
	LIMK2	ENST00000887560.1		c.*758A>C		3_prime_UTR	Exon 17 of 17	ENSP00000557619.1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120424 AN: 152090 Hom.: 48620 Cov.: 33

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.808

GnomAD4 exome AF: 0.750 AC: 30 AN: 40 Hom.: 12 Cov.: 0 AF XY: 0.846 AC XY: 22 AN XY: 26

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.700 AC: 7 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 15 AN: 20

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.792 AC: 120532 AN: 152208 Hom.: 48673 Cov.: 33 AF XY: 0.790 AC XY: 58784 AN XY: 74406

African (AFR) AF: 0.947 AC: 39360 AN: 41546

American (AMR) AF: 0.762 AC: 11648 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2802 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4534 AN: 5164

South Asian (SAS) AF: 0.788 AC: 3804 AN: 4826

European-Finnish (FIN) AF: 0.678 AC: 7175 AN: 10586

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48598 AN: 68008

Other (OTH) AF: 0.810 AC: 1710 AN: 2112

Alfa AF: 0.746 Hom.: 75855

Bravo AF: 0.806

Asia WGS AF: 0.861 AC: 2992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		0.77
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: rs4141404; hg19: chr22-31675185;