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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02649	ENST00000659311.1	n.623-3808G>A		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.633

Alfa AF: 0.701 Hom.: 44844

Bravo AF: 0.586

Asia WGS AF: 0.631 AC: 2194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2181622; hg19: chr10-6391061;