rs141196718

Variant names:

• chr1-62210002-C-A
• rs141196718
• NM_019079.5:c.1228C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-62210002-C-A
• chr1-62210002-C-G
• chr1-62210002-C-T

Variant summary

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

The NM_019079.5(L1TD1):​c.1228C>A​(p.Pro410Thr) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P410S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: L1TD1 NM_019079.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 4 publications found

Genes affected

L1TD1 (HGNC:25595): (LINE1 type transposase domain containing 1) Predicted to enable single-stranded RNA binding activity. Predicted to be involved in transposition, RNA-mediated. Located in intracellular membrane-bounded organelle. [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 (MetaRNN=0.027809262).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019079.5. 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
	L1TD1	NM_019079.5	MANE Select	c.1228C>A	p.Pro410Thr	missense	Exon 4 of 4	NP_061952.3
	L1TD1	NM_001164835.2		c.1228C>A	p.Pro410Thr	missense	Exon 5 of 5	NP_001158307.1	Q5T7N2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	L1TD1	ENST00000498273.2	TSL:1 MANE Select	c.1228C>A	p.Pro410Thr	missense	Exon 4 of 4	ENSP00000419901.1	Q5T7N2
	L1TD1	ENST00000928897.1		c.1228C>A	p.Pro410Thr	missense	Exon 5 of 5	ENSP00000598956.1
	L1TD1	ENST00000928898.1		c.1228C>A	p.Pro410Thr	missense	Exon 4 of 4	ENSP00000598957.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 44

GnomAD4 genome Cov.: 31

Alfa AF: 0.000152 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.027
DANN	Benign	0.71
DEOGEN2	Benign	0.022	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0063	N
LIST_S2	Benign	0.35	T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.028	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.34	N
PhyloP100		-1.2
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.43	N
REVEL	Benign	0.0040
Sift	Benign	0.81	T
Sift4G	Benign	0.29	T
Polyphen		0.0	B
Vest4		0.048
MVP		0.061
MPC		0.044
ClinPred		0.026	T
GERP RS		-2.0
Varity_R		0.027
gMVP		0.014
Mutation Taster		=98/2	polymorphism

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: rs141196718; hg19: chr1-62675674; COSMIC: COSV63133430; COSMIC: COSV63133430;