rs6518219

Positions:

• chr21-45234802-A-T

Variant summary

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

The NR_135279.1(LINC00334):​n.167+296A>T variant causes a intron, non coding transcript 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 NR_135279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00334	NR_135279.1	n.167+296A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00334	ENST00000660971.1	n.169+326A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.150

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6518219; hg19: chr21-46654717;