rs2340442

Variant names:

• chr12-25490209-G-A
• rs2340442
• NM_001145728.2:c.*22+13529C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-25490209-G-A
• chr12-25490209-G-C
• chr12-25490209-G-T

Variant summary

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

The NM_001145728.2(LMNTD1):​c.*22+13529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,272 control chromosomes in the GnomAD database, including 67,364 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 0.94 (67364 hom., cov: 33)
• Consequence: LMNTD1 NM_001145728.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

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.*22+13529C>T		intron	N/A	NP_001139200.1	Q8N9Z9-5
	LMNTD1	NM_152590.3		c.*22+13529C>T		intron	N/A	NP_689803.2	Q8N9Z9-1
	LMNTD1	NM_001256266.1		c.*22+13529C>T		intron	N/A	NP_001243195.1	Q8N9Z9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMNTD1	ENST00000458174.7	TSL:2 MANE Select	c.*22+13529C>T		intron	N/A	ENSP00000407353.2	Q8N9Z9-5
	LMNTD1	ENST00000539744.5	TSL:1	c.*22+13529C>T		intron	N/A	ENSP00000443132.1	Q8N9Z9-2
	LMNTD1	ENST00000282881.10	TSL:2	c.*22+13529C>T		intron	N/A	ENSP00000282881.6	Q8N9Z9-1

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142880 AN: 152154 Hom.: 67312 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.939 AC: 142991 AN: 152272 Hom.: 67364 Cov.: 33 AF XY: 0.937 AC XY: 69751 AN XY: 74458

African (AFR) AF: 0.854 AC: 35452 AN: 41524

American (AMR) AF: 0.968 AC: 14817 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3437 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5124 AN: 5184

South Asian (SAS) AF: 0.949 AC: 4580 AN: 4826

European-Finnish (FIN) AF: 0.913 AC: 9683 AN: 10600

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66686 AN: 68040

Other (OTH) AF: 0.952 AC: 2015 AN: 2116

Alfa AF: 0.974 Hom.: 70431

Bravo AF: 0.941

Asia WGS AF: 0.967 AC: 3354 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.4
DANN	Benign	0.54
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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: rs2340442; hg19: chr12-25643143;