rs771067474

Variant names:

• chr3-8537345-C-A
• rs771067474
• NM_014583.4:c.292C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-8537345-C-A
• chr3-8537345-C-G
• chr3-8537345-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014583.4(LMCD1):​c.292C>A​(p.Arg98Arg) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LMCD1 NM_014583.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.79

Genes affected

LMCD1 (HGNC:6633): (LIM and cysteine rich domains 1) This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

LMCD1-AS1 (HGNC:44477): (LMCD1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMCD1	NM_014583.4	c.292C>A	p.Arg98Arg	synonymous_variant	Exon 3 of 6	ENST00000157600.8	NP_055398.1
LMCD1	NM_001278233.2	c.73C>A	p.Arg25Arg	synonymous_variant	Exon 2 of 5		NP_001265162.1
LMCD1	NM_001278235.2	c.292C>A	p.Arg98Arg	synonymous_variant	Exon 3 of 5		NP_001265164.1
LMCD1	NM_001278234.2	c.51+4520C>A		intron_variant	Intron 2 of 4		NP_001265163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMCD1	ENST00000157600.8	c.292C>A	p.Arg98Arg	synonymous_variant	Exon 3 of 6	1	NM_014583.4	ENSP00000157600.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.080
CADD	Benign	13
DANN	Benign	0.87

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: rs771067474; hg19: chr3-8579031;