21-32146850-G-T

Variant names:

• chr21-32146850-G-T
• rs2833681
• ENST00000411605.6:n.127-60552C>A

Variant summary

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

The ENST00000411605.6(LINC00159):​n.127-60552C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 152,300 control chromosomes in the GnomAD database, including 69,698 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 0.96 (69698 hom., cov: 33)
• Consequence: LINC00159 ENST00000411605.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 1 publications found

Genes affected

LINC00159 (HGNC:1285): (long intergenic non-protein coding RNA 159)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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
LINC00159	ENST00000411605.6	n.127-60552C>A		intron_variant	Intron 2 of 4	3
LINC00159	ENST00000414877.1	n.134+9558C>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.956 AC: 145420 AN: 152182 Hom.: 69652 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.956 AC: 145524 AN: 152300 Hom.: 69698 Cov.: 33 AF XY: 0.956 AC XY: 71230 AN XY: 74476

African (AFR) AF: 0.885 AC: 36770 AN: 41528

American (AMR) AF: 0.966 AC: 14786 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3409 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4992 AN: 5194

South Asian (SAS) AF: 0.972 AC: 4690 AN: 4824

European-Finnish (FIN) AF: 0.997 AC: 10581 AN: 10612

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67131 AN: 68044

Other (OTH) AF: 0.959 AC: 2027 AN: 2114

Alfa AF: 0.977 Hom.: 72744

Bravo AF: 0.949

Asia WGS AF: 0.973 AC: 3383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2833681; hg19: chr21-33519161;