21-33981573-G-T

Variant names:

• chr21-33981573-G-T
• rs2070513
• ENST00000813276.1:n.243-21238G>T

Variant summary

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

The ENST00000813276.1(LINC00649):​n.243-21238G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,926 control chromosomes in the GnomAD database, including 12,142 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 0.38 (12142 hom., cov: 31)
• Consequence: LINC00649 ENST00000813276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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
LINC00649	ENST00000813276.1	n.243-21238G>T		intron_variant	Intron 2 of 2
LINC00649	ENST00000813277.1	n.80+5022G>T		intron_variant	Intron 1 of 2
LINC00649	ENST00000813295.1	n.108+5022G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57535 AN: 151808 Hom.: 12117 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.379 AC: 57599 AN: 151926 Hom.: 12142 Cov.: 31 AF XY: 0.372 AC XY: 27622 AN XY: 74270

African (AFR) AF: 0.573 AC: 23728 AN: 41394

American (AMR) AF: 0.402 AC: 6141 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1658 AN: 5154

South Asian (SAS) AF: 0.326 AC: 1563 AN: 4794

European-Finnish (FIN) AF: 0.206 AC: 2174 AN: 10574

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20059 AN: 67952

Other (OTH) AF: 0.375 AC: 793 AN: 2112

Alfa AF: 0.251 Hom.: 881

Bravo AF: 0.408

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.019
DANN	Benign	0.64
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2070513; hg19: chr21-35353874;