rs2769261

chr1-113024285-C-A

Variant summary

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

The NR_103777.1(LRIG2-DT):n.304-10446G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,948 control chromosomes in the GnomAD database, including 3,645 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 0.20 (3645 hom., cov: 31)
• Consequence: LRIG2-DT NR_103777.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

LRIG2-DT (HGNC:54312): (LRIG2 divergent transcript)

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIG2-DT	NR_103777.1	n.304-10446G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIG2-DT	ENST00000421157.2	n.315-10446G>T		intron_variant, non_coding_transcript_variant		1
SLC16A1-AS1	ENST00000627431.2	n.644-9390C>A		intron_variant, non_coding_transcript_variant		5
SLC16A1-AS1	ENST00000413231.5	n.107+15925C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30477 AN: 151828 Hom.: 3647 Cov.: 31

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30460 AN: 151948 Hom.: 3645 Cov.: 31 AF XY: 0.201 AC XY: 14891 AN XY: 74256

Gnomad4 AFR AF: 0.0770

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.200

Alfa AF: 0.244 Hom.: 1835

Bravo AF: 0.192

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2769261; hg19: chr1-113566907;