rs6656763

Positions:

• chr1-62196120-G-A
• chr1-62196120-G-T

Variant summary

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

The NM_019079.5(L1TD1):​c.-204-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,022 control chromosomes in the GnomAD database, including 40,276 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 0.73 (40276 hom., cov: 32)
• Consequence: L1TD1 NM_019079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
L1TD1	NM_019079.5	c.-204-315G>A		intron_variant		ENST00000498273.2
L1TD1	NM_001164835.2	c.-315-315G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
L1TD1	ENST00000498273.2	c.-204-315G>A		intron_variant		1	NM_019079.5	P1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110459 AN: 151908 Hom.: 40225 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.727 AC: 110559 AN: 152022 Hom.: 40276 Cov.: 32 AF XY: 0.724 AC XY: 53797 AN XY: 74294

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.740

Alfa AF: 0.718 Hom.: 17765

Bravo AF: 0.737

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs6656763; hg19: chr1-62661792;