rs6518219

Variant names:

• chr21-45234802-A-T
• rs6518219
• ENST00000757339.1:n.489A>T

Variant summary

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

The ENST00000757339.1(LINC00334):​n.489A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,220 control chromosomes in the GnomAD database, including 2,494 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 0.14 (2494 hom., cov: 32)
• Consequence: LINC00334 ENST00000757339.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 4 publications found

Genes affected

LINC00334 (HGNC:16425): (long intergenic non-protein coding RNA 334)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00334	NR_135279.1	n.167+296A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00334	ENST00000757339.1	n.489A>T		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00334	ENST00000328344.2	n.155+296A>T		intron_variant	Intron 1 of 2	2
LINC00334	ENST00000584169.5	n.137+326A>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21722 AN: 152102 Hom.: 2482 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.143 AC: 21776 AN: 152220 Hom.: 2494 Cov.: 32 AF XY: 0.142 AC XY: 10558 AN XY: 74434

African (AFR) AF: 0.310 AC: 12863 AN: 41510

American (AMR) AF: 0.110 AC: 1684 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3466

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5164

South Asian (SAS) AF: 0.141 AC: 683 AN: 4830

European-Finnish (FIN) AF: 0.0493 AC: 523 AN: 10616

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3747 AN: 68020

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.100 Hom.: 179

Bravo AF: 0.156

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.88
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6518219; hg19: chr21-46654717;