rs2304136

Positions:

• chr19-48139867-T-C

Variant summary

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

The NM_000234.3(LIG1):​c.1087+104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 1,354,896 control chromosomes in the GnomAD database, including 10,713 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 0.17 (4045 hom., cov: 32)
  • Exomes 𝑓: 0.079 (6668 hom.)
• Consequence: LIG1 NM_000234.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.98

Genes affected

LIG1 (HGNC:6598): (DNA ligase 1) This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents. Disruption of this gene may also be associated with a variety of cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

LIG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIG1	NM_000234.3	c.1087+104A>G		intron_variant		ENST00000263274.12	NP_000225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIG1	ENST00000263274.12	c.1087+104A>G		intron_variant		1	NM_000234.3	ENSP00000263274.6

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26055 AN: 151992 Hom.: 4033 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.0790 AC: 95067 AN: 1202786 Hom.: 6668 AF XY: 0.0803 AC XY: 49024 AN XY: 610664

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.0920

Gnomad4 ASJ exome AF: 0.0852

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.148

Gnomad4 FIN exome AF: 0.0673

Gnomad4 NFE exome AF: 0.0537

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.172 AC: 26097 AN: 152110 Hom.: 4045 Cov.: 32 AF XY: 0.169 AC XY: 12591 AN XY: 74366

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0888

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0767 Hom.: 985

Bravo AF: 0.186

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.38

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: rs2304136; hg19: chr19-48643124; COSMIC: COSV54390221; COSMIC: COSV54390221;