rs4345220

Variant names:

• chr4-41637499-A-C
• rs4345220
• NM_001330672.2:c.2091-1433A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-41637499-A-C
• chr4-41637499-A-G
• chr4-41637499-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001330672.2(LIMCH1):​c.2091-1433A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: LIMCH1 NM_001330672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 5 publications found

Genes affected

LIMCH1 (HGNC:29191): (LIM and calponin homology domains 1) Enables myosin II head/neck binding activity. Involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Located in stress fiber. Colocalizes with myosin II complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330672.2. 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
	LIMCH1	NM_001330672.2	MANE Select	c.2091-1433A>C		intron	N/A	NP_001317601.1
	LIMCH1	NM_001330787.2		c.936-1433A>C		intron	N/A	NP_001317716.1
	LIMCH1	NM_014988.5		c.936-1433A>C		intron	N/A	NP_055803.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIMCH1	ENST00000503057.6	TSL:1 MANE Select	c.2091-1433A>C		intron	N/A	ENSP00000425631.1
	LIMCH1	ENST00000313860.12	TSL:1	c.936-1433A>C		intron	N/A	ENSP00000316891.7
	LIMCH1	ENST00000512820.5	TSL:1	c.936-7001A>C		intron	N/A	ENSP00000424437.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 60658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.81
DANN	Benign	0.70
PhyloP100		-0.35

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: rs4345220; hg19: chr4-41639516;