NM_001145728.2:c.1190-3845T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145728.2(LMNTD1):​c.1190-3845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,054 control chromosomes in the GnomAD database, including 33,108 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 0.66 (33108 hom., cov: 31)
• Consequence: LMNTD1 NM_001145728.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMNTD1	NM_001145728.2	c.1190-3845T>C		intron_variant	Intron 8 of 9	ENST00000458174.7	NP_001139200.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMNTD1	ENST00000458174.7	c.1190-3845T>C		intron_variant	Intron 8 of 9	2	NM_001145728.2	ENSP00000407353.2

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99585 AN: 151936 Hom.: 33083 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.655 AC: 99660 AN: 152054 Hom.: 33108 Cov.: 31 AF XY: 0.655 AC XY: 48655 AN XY: 74314

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.663

Alfa AF: 0.685 Hom.: 8505

Bravo AF: 0.651

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.023
DANN	Benign	0.41

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: rs10743565; hg19: chr12-25660579;