NM_170707.4:c.-3_12delGCCATGGAGACCCCG

Variant names:

• chr1-156114912-GCCGGCCATGGAGACC-G
• rs267607546
• NM_170707.4:c.-3_12delGCCATGGAGACCCCG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PS1_Moderate PM2

The NM_170707.4(LMNA):​c.-3_12delGCCATGGAGACCCCG​(p.Met1_Pro4del) variant causes a start lost, conservative inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LMNA NM_170707.4 start_lost, conservative_inframe_deletion
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 7.06

Genes affected

LMNA (HGNC:6636): (lamin A/C) The protein encoded by this gene is part of the nuclear lamina, a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PS1: Another start lost variant in NM_170707.4 (LMNA) was described as [Likely_pathogenic] in ClinVar as 200949
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMNA	NM_170707.4	c.-3_12delGCCATGGAGACCCCG	p.Met1_Pro4del	start_lost, conservative_inframe_deletion	Exon 1 of 12	ENST00000368300.9	NP_733821.1
LMNA	NM_005572.4	c.-3_12delGCCATGGAGACCCCG	p.Met1_Pro4del	start_lost, conservative_inframe_deletion	Exon 1 of 10	ENST00000677389.1	NP_005563.1
LMNA	NM_170707.4	c.-3_12delGCCATGGAGACCCCG		5_prime_UTR_variant	Exon 1 of 12	ENST00000368300.9	NP_733821.1
LMNA	NM_005572.4	c.-3_12delGCCATGGAGACCCCG		5_prime_UTR_variant	Exon 1 of 10	ENST00000677389.1	NP_005563.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMNA	ENST00000368300.9	c.-3_12delGCCATGGAGACCCCG	p.Met1_Pro4del	start_lost, conservative_inframe_deletion	Exon 1 of 12	1	NM_170707.4	ENSP00000357283.4
LMNA	ENST00000677389.1	c.-3_12delGCCATGGAGACCCCG	p.Met1_Pro4del	start_lost, conservative_inframe_deletion	Exon 1 of 10		NM_005572.4	ENSP00000503633.1
LMNA	ENST00000368300	c.-3_12delGCCATGGAGACCCCG		5_prime_UTR_variant	Exon 1 of 12	1	NM_170707.4	ENSP00000357283.4
LMNA	ENST00000677389	c.-3_12delGCCATGGAGACCCCG		5_prime_UTR_variant	Exon 1 of 10		NM_005572.4	ENSP00000503633.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

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Epithelial Biology; Institute of Medical Biology, Singapore

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267607546; hg19: chr1-156084703;