rs2769261

Variant names:

• chr1-113024285-C-A
• rs2769261
• ENST00000421157.2:n.315-10446G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421157.2(LRIG2-DT):​n.315-10446G>T variant causes a intron 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 ENST00000421157.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 5 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421157.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRIG2-DT	NR_103777.1		n.304-10446G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRIG2-DT	ENST00000421157.2	TSL:1	n.315-10446G>T		intron	N/A
	SLC16A1-AS1	ENST00000413231.6	TSL:2	n.1072+15925C>A		intron	N/A
	SLC16A1-AS1	ENST00000627431.2	TSL:5	n.644-9390C>A		intron	N/A

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

African (AFR) AF: 0.0770 AC: 3196 AN: 41486

American (AMR) AF: 0.211 AC: 3216 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3462

East Asian (EAS) AF: 0.134 AC: 692 AN: 5154

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4812

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10554

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17929 AN: 67938

Other (OTH) AF: 0.200 AC: 420 AN: 2104

Alfa AF: 0.241 Hom.: 2161

Bravo AF: 0.192

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2769261; hg19: chr1-113566907;