chr1-113058823-C-A

Variant names:

• chr1-113058823-C-A
• rs2798686
• ENST00000421157.2:n.176-10262G>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.176-10262G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,014 control chromosomes in the GnomAD database, including 15,974 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 0.45 (15974 hom., cov: 32)
• Consequence: LRIG2-DT ENST00000421157.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIG2-DT	NR_103777.1	n.165-10262G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRIG2-DT	ENST00000421157.2	n.176-10262G>T		intron_variant	Intron 1 of 2	1
LRIG2-DT	ENST00000765033.1	n.152-10262G>T		intron_variant	Intron 1 of 2
LRIG2-DT	ENST00000765034.1	n.141+14140G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67819 AN: 151896 Hom.: 15953 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.447 AC: 67881 AN: 152014 Hom.: 15974 Cov.: 32 AF XY: 0.448 AC XY: 33300 AN XY: 74292

African (AFR) AF: 0.577 AC: 23926 AN: 41472

American (AMR) AF: 0.417 AC: 6354 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1778 AN: 3466

East Asian (EAS) AF: 0.693 AC: 3572 AN: 5158

South Asian (SAS) AF: 0.461 AC: 2226 AN: 4824

European-Finnish (FIN) AF: 0.369 AC: 3899 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24599 AN: 67950

Other (OTH) AF: 0.439 AC: 929 AN: 2114

Alfa AF: 0.393 Hom.: 38437

Bravo AF: 0.458

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2798686; hg19: chr1-113601445;