NM_014583.4:c.43-3313G>A

Variant names:

• chr3-8529424-G-A
• rs9831647
• NM_014583.4:c.43-3313G>A

Variant summary

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

The NM_014583.4(LMCD1):​c.43-3313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,988 control chromosomes in the GnomAD database, including 11,931 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 0.38 (11931 hom., cov: 33)
• Consequence: LMCD1 NM_014583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMCD1	NM_014583.4	c.43-3313G>A		intron_variant	Intron 1 of 5	ENST00000157600.8	NP_055398.1
LMCD1	NM_001278233.2	c.-88-7761G>A		intron_variant	Intron 1 of 4		NP_001265162.1
LMCD1	NM_001278234.2	c.-38-3313G>A		intron_variant	Intron 1 of 4		NP_001265163.1
LMCD1	NM_001278235.2	c.43-3313G>A		intron_variant	Intron 1 of 4		NP_001265164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMCD1	ENST00000157600.8	c.43-3313G>A		intron_variant	Intron 1 of 5	1	NM_014583.4	ENSP00000157600.3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57376 AN: 151870 Hom.: 11936 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.378 AC: 57379 AN: 151988 Hom.: 11931 Cov.: 33 AF XY: 0.369 AC XY: 27370 AN XY: 74268

African (AFR) AF: 0.259 AC: 10744 AN: 41428

American (AMR) AF: 0.332 AC: 5075 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3466

East Asian (EAS) AF: 0.0567 AC: 293 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4286 AN: 10548

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33178 AN: 67958

Other (OTH) AF: 0.386 AC: 815 AN: 2112

Alfa AF: 0.424 Hom.: 22813

Bravo AF: 0.366

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.79
PhyloP100		0.76
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: rs9831647; hg19: chr3-8571110;