rs2167037

Variant names:

• chr3-8508677-C-A
• rs2167037
• NM_014583.4:c.42+6697C>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.42+6697C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,046 control chromosomes in the GnomAD database, including 17,000 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 0.46 (17000 hom., cov: 33)
• Consequence: LMCD1 NM_014583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014583.4. 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
	LMCD1	NM_014583.4	MANE Select	c.42+6697C>A		intron	N/A	NP_055398.1	Q9NZU5-1
	LMCD1	NM_001278233.2		c.-89+6697C>A		intron	N/A	NP_001265162.1	Q9NZU5-2
	LMCD1	NM_001278234.2		c.-39+6697C>A		intron	N/A	NP_001265163.1	B4DEY6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMCD1	ENST00000157600.8	TSL:1 MANE Select	c.42+6697C>A		intron	N/A	ENSP00000157600.3	Q9NZU5-1
	LMCD1	ENST00000880274.1		c.42+6697C>A		intron	N/A	ENSP00000550333.1
	LMCD1	ENST00000957327.1		c.42+6697C>A		intron	N/A	ENSP00000627386.1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70417 AN: 151928 Hom.: 17002 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0663

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.463 AC: 70445 AN: 152046 Hom.: 17000 Cov.: 33 AF XY: 0.455 AC XY: 33801 AN XY: 74326

African (AFR) AF: 0.468 AC: 19412 AN: 41438

American (AMR) AF: 0.372 AC: 5691 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3466

East Asian (EAS) AF: 0.0664 AC: 344 AN: 5178

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4820

European-Finnish (FIN) AF: 0.445 AC: 4705 AN: 10572

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35279 AN: 67980

Other (OTH) AF: 0.455 AC: 959 AN: 2108

Alfa AF: 0.488 Hom.: 2415

Bravo AF: 0.455

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.32
PhyloP100		-1.6
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: rs2167037; hg19: chr3-8550363;