rs7970954

chr12-25642173-T-C

Variant summary

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

The NM_001352232.2(LMNTD1):c.-283+6321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,992 control chromosomes in the GnomAD database, including 19,986 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 0.48 (19986 hom., cov: 31)
• Consequence: LMNTD1 NM_001352232.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMNTD1	NM_001145727.3	c.58+6321A>G		intron_variant
LMNTD1	NM_001352232.2	c.-283+6321A>G		intron_variant
LMNTD1	NM_001352233.2	c.-92+6321A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMNTD1	ENST00000445693.5	c.58+6321A>G		intron_variant		2		A2
LMNTD1	ENST00000540106.5	c.-50+6321A>G		intron_variant		4
LMNTD1	ENST00000542224.1	c.-223+6321A>G		intron_variant		5
LMNTD1	ENST00000545543.1	c.-83+6321A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72964 AN: 151874 Hom.: 19993 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.480 AC: 72976 AN: 151992 Hom.: 19986 Cov.: 31 AF XY: 0.478 AC XY: 35480 AN XY: 74300

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.506

Alfa AF: 0.599 Hom.: 45860

Bravo AF: 0.468

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7970954; hg19: chr12-25795107;