chr12-25618961-A-G

Variant names:

• chr12-25618961-A-G
• rs7139066
• NM_001352232.2:c.-283+29533T>C

Variant summary

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

The NM_001352232.2(LMNTD1):​c.-283+29533T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,920 control chromosomes in the GnomAD database, including 22,906 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 0.53 (22906 hom., cov: 30)
• Consequence: LMNTD1 NM_001352232.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 2 publications found

Genes affected

LMNTD1 (HGNC:26683): (lamin tail domain containing 1) Predicted to act upstream of or within cell population proliferation. Predicted to be located in nucleus. Predicted to be active in cytoplasm and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352232.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMNTD1	NM_001352232.2		c.-283+29533T>C		intron	N/A	NP_001339161.1
	LMNTD1	NM_001352233.2		c.-92+29533T>C		intron	N/A	NP_001339162.1
	LMNTD1	NM_001352234.2		c.-50+29533T>C		intron	N/A	NP_001339163.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMNTD1	ENST00000445693.5	TSL:2	c.58+29533T>C		intron	N/A	ENSP00000407043.1
	LMNTD1	ENST00000538178.5	TSL:3	c.-50+11634T>C		intron	N/A	ENSP00000442871.1
	LMNTD1	ENST00000540106.5	TSL:4	c.-50+29533T>C		intron	N/A	ENSP00000445242.1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80534 AN: 151802 Hom.: 22894 Cov.: 30

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.530 AC: 80579 AN: 151920 Hom.: 22906 Cov.: 30 AF XY: 0.529 AC XY: 39238 AN XY: 74198

African (AFR) AF: 0.341 AC: 14123 AN: 41432

American (AMR) AF: 0.594 AC: 9067 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5172

South Asian (SAS) AF: 0.511 AC: 2456 AN: 4810

European-Finnish (FIN) AF: 0.595 AC: 6263 AN: 10518

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43576 AN: 67946

Other (OTH) AF: 0.564 AC: 1187 AN: 2106

Alfa AF: 0.599 Hom.: 84376

Bravo AF: 0.524

Asia WGS AF: 0.422 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.50
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7139066; hg19: chr12-25771895;