rs6089829

Variant names:

• chr20-63037684-A-G
• rs6089829
• ENST00000606208.5:n.91+28211A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606208.5(LINC01749):​n.91+28211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,106 control chromosomes in the GnomAD database, including 30,310 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 0.63 (30310 hom., cov: 34)
• Consequence: LINC01749 ENST00000606208.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LINC01749 (HGNC:52537): (long intergenic non-protein coding RNA 1749)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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
LINC01749	ENST00000606208.5	n.91+28211A>G		intron_variant	Intron 1 of 1	1
LINC01749	ENST00000607802.1	n.91+28211A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95476 AN: 151988 Hom.: 30279 Cov.: 34

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.628 AC: 95555 AN: 152106 Hom.: 30310 Cov.: 34 AF XY: 0.628 AC XY: 46723 AN XY: 74370

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.655

Alfa AF: 0.643 Hom.: 40865

Bravo AF: 0.635

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6089829; hg19: chr20-61669036;