rs10743565

Variant names:

• chr12-25507645-A-C
• rs10743565
• NM_001145728.2:c.1190-3845T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-25507645-A-C
• chr12-25507645-A-G
• chr12-25507645-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001145728.2(LMNTD1):​c.1190-3845T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LMNTD1 NM_001145728.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145728.2. 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
	LMNTD1	NM_001145728.2	MANE Select	c.1190-3845T>G		intron	N/A	NP_001139200.1	Q8N9Z9-5
	LMNTD1	NM_152590.3		c.1127-3845T>G		intron	N/A	NP_689803.2	Q8N9Z9-1
	LMNTD1	NM_001145729.1		c.1070-3845T>G		intron	N/A	NP_001139201.1	Q8N9Z9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMNTD1	ENST00000458174.7	TSL:2 MANE Select	c.1190-3845T>G		intron	N/A	ENSP00000407353.2	Q8N9Z9-5
	LMNTD1	ENST00000413632.6	TSL:1	c.1070-3845T>G		intron	N/A	ENSP00000393150.2	Q8N9Z9-4
	LMNTD1	ENST00000539744.5	TSL:1	c.836-3845T>G		intron	N/A	ENSP00000443132.1	Q8N9Z9-2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.020
DANN	Benign	0.46
PhyloP100		-1.9

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: rs10743565; hg19: chr12-25660579;