chr21-43359800-C-T

Variant names:

• chr21-43359800-C-T
• rs496300
• ENST00000442815.1:n.1459-314G>A

Variant summary

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

The ENST00000442815.1(LINC01679):​n.1459-314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,138 control chromosomes in the GnomAD database, including 41,654 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 0.73 (41654 hom., cov: 33)
• Consequence: LINC01679 ENST00000442815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

LINC01679 (HGNC:52469): (long intergenic non-protein coding RNA 1679)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01679	NR_131902.1	n.1459-314G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01679	ENST00000442815.1	n.1459-314G>A		intron_variant	Intron 1 of 1	3
LINC01679	ENST00000689953.1	n.341-314G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110588 AN: 152020 Hom.: 41581 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.728 AC: 110722 AN: 152138 Hom.: 41654 Cov.: 33 AF XY: 0.727 AC XY: 54047 AN XY: 74386

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.739

Alfa AF: 0.655 Hom.: 74332

Bravo AF: 0.754

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs496300; hg19: chr21-44779680;