rs2167037

Positions:

• chr3-8508677-C-A

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMCD1	NM_014583.4	c.42+6697C>A		intron_variant		ENST00000157600.8	NP_055398.1
LMCD1	NM_001278233.2	c.-89+6697C>A		intron_variant			NP_001265162.1
LMCD1	NM_001278234.2	c.-39+6697C>A		intron_variant			NP_001265163.1
LMCD1	NM_001278235.2	c.42+6697C>A		intron_variant			NP_001265164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMCD1	ENST00000157600.8	c.42+6697C>A		intron_variant		1	NM_014583.4	ENSP00000157600.3

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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.455

Alfa AF: 0.488 Hom.: 2317

Bravo AF: 0.455

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.32

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: rs2167037; hg19: chr3-8550363;