rs10497055

Variant names:

• chr2-150340810-G-A
• rs10497055
• ENST00000659082.1:n.408-13244G>A

Variant summary

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

The ENST00000659082.1(LINC01818):​n.408-13244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,216 control chromosomes in the GnomAD database, including 1,047 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 0.071 (1047 hom., cov: 32)
• Consequence: LINC01818 ENST00000659082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 1 publications found

Genes affected

LINC01818 (HGNC:52623): (long intergenic non-protein coding RNA 1818)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01818	NR_187171.1	n.393-13244G>A		intron_variant	Intron 3 of 4
LINC01818	NR_187172.1	n.231-13244G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01818	ENST00000659082.1	n.408-13244G>A		intron_variant	Intron 3 of 4
LINC01818	ENST00000665690.1	n.201-13244G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10716 AN: 152098 Hom.: 1042 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0706 AC: 10745 AN: 152216 Hom.: 1047 Cov.: 32 AF XY: 0.0687 AC XY: 5116 AN XY: 74426

African (AFR) AF: 0.218 AC: 9029 AN: 41482

American (AMR) AF: 0.0269 AC: 411 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3468

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5186

South Asian (SAS) AF: 0.0306 AC: 148 AN: 4830

European-Finnish (FIN) AF: 0.0252 AC: 267 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 746 AN: 68026

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.0539 Hom.: 170

Bravo AF: 0.0778

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10497055; hg19: chr2-151197324;