rs6089829

chr20-63037684-A-G

Variant summary

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

The NR_033370.1(LINC01749):n.91+28211A>G variant causes a intron, non coding transcript 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 NR_033370.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt
LINC01749	NR_033370.1	n.91+28211A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01749	ENST00000606208.5	n.91+28211A>G		intron_variant, non_coding_transcript_variant		1
LINC01749	ENST00000607802.1	n.91+28211A>G		intron_variant, non_coding_transcript_variant		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;