rs10196529

Variant names:

• chr2-22253108-A-G
• rs10196529
• ENST00000450551.1:n.71-42114T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-22253108-A-G
• chr2-22253108-A-T

Variant summary

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

The ENST00000450551.1(LINC01830):​n.71-42114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,034 control chromosomes in the GnomAD database, including 591 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 0.053 (591 hom., cov: 32)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450551.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01830	ENST00000450551.1	TSL:5	n.71-42114T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7998 AN: 151916 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00752

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0527 AC: 8015 AN: 152034 Hom.: 591 Cov.: 32 AF XY: 0.0512 AC XY: 3804 AN XY: 74334

African (AFR) AF: 0.162 AC: 6733 AN: 41498

American (AMR) AF: 0.0272 AC: 415 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3470

East Asian (EAS) AF: 0.000779 AC: 4 AN: 5136

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4828

European-Finnish (FIN) AF: 0.000659 AC: 7 AN: 10624

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00752 AC: 511 AN: 67914

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0223 Hom.: 68

Bravo AF: 0.0603

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.64
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10196529; hg19: chr2-22475980;