chr2-22677249-G-A

Variant names:

• chr2-22677249-G-A
• rs10495728
• ENST00000833262.1:n.100+17516C>T

Variant summary

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

The ENST00000833262.1(LINC01830):​n.100+17516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,098 control chromosomes in the GnomAD database, including 5,315 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 0.24 (5315 hom., cov: 32)
• Consequence: LINC01830 ENST00000833262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 publications found

Genes affected

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833262.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01830	ENST00000833262.1		n.100+17516C>T		intron	N/A
	LINC01830	ENST00000833263.1		n.118+17516C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37166 AN: 151980 Hom.: 5305 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.244 AC: 37184 AN: 152098 Hom.: 5315 Cov.: 32 AF XY: 0.251 AC XY: 18622 AN XY: 74338

African (AFR) AF: 0.100 AC: 4151 AN: 41522

American (AMR) AF: 0.307 AC: 4692 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2200 AN: 5172

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3896 AN: 10566

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18993 AN: 67974

Other (OTH) AF: 0.276 AC: 581 AN: 2104

Alfa AF: 0.265 Hom.: 17679

Bravo AF: 0.238

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.32
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10495728; hg19: chr2-22900121;