21-33982222-T-C

Variant names:

• chr21-33982222-T-C
• rs2032314
• ENST00000813276.1:n.243-20589T>C

Variant summary

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

The ENST00000813276.1(LINC00649):​n.243-20589T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,070 control chromosomes in the GnomAD database, including 57,180 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 0.86 (57180 hom., cov: 30)
• Consequence: LINC00649 ENST00000813276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 24 publications found

Genes affected

LINC00649 (HGNC:44305): (long intergenic non-protein coding RNA 649)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813276.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00649	ENST00000813276.1		n.243-20589T>C		intron	N/A
	LINC00649	ENST00000813277.1		n.80+5671T>C		intron	N/A
	LINC00649	ENST00000813295.1		n.108+5671T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131108 AN: 151952 Hom.: 57153 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.863 AC: 131187 AN: 152070 Hom.: 57180 Cov.: 30 AF XY: 0.864 AC XY: 64244 AN XY: 74342

African (AFR) AF: 0.733 AC: 30374 AN: 41422

American (AMR) AF: 0.877 AC: 13395 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3893 AN: 5168

South Asian (SAS) AF: 0.888 AC: 4278 AN: 4816

European-Finnish (FIN) AF: 0.947 AC: 10017 AN: 10576

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63314 AN: 68028

Other (OTH) AF: 0.874 AC: 1848 AN: 2114

Alfa AF: 0.903 Hom.: 269240

Bravo AF: 0.849

Asia WGS AF: 0.847 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.41
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2032314; hg19: chr21-35354523;