rs2181622

Variant names:

• chr10-6349099-G-A
• rs2181622
• ENST00000659311.1:n.623-3808G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-6349099-G-A
• chr10-6349099-G-C

Variant summary

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

The ENST00000659311.1(LINC02649):​n.623-3808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,038 control chromosomes in the GnomAD database, including 29,668 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 0.60 (29668 hom., cov: 32)
• Consequence: LINC02649 ENST00000659311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 5 publications found

Genes affected

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

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 (AMR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02649	ENST00000659311.1		n.623-3808G>A		intron	N/A
	LINC02649	ENST00000783921.1		n.405+4319G>A		intron	N/A
	LINC02649	ENST00000783922.1		n.423-3808G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90634 AN: 151920 Hom.: 29658 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.596 AC: 90660 AN: 152038 Hom.: 29668 Cov.: 32 AF XY: 0.598 AC XY: 44426 AN XY: 74302

African (AFR) AF: 0.297 AC: 12288 AN: 41424

American (AMR) AF: 0.726 AC: 11109 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2416 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3407 AN: 5166

South Asian (SAS) AF: 0.654 AC: 3154 AN: 4822

European-Finnish (FIN) AF: 0.647 AC: 6836 AN: 10560

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49248 AN: 67986

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.687 Hom.: 53842

Bravo AF: 0.586

Asia WGS AF: 0.631 AC: 2194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.59
PhyloP100		-0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2181622;

hg19: chr10-6391061;