rs2838824

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_135279.1(LINC00334):​n.167+964G>A 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 0.108 in 152,148 control chromosomes in the GnomAD database, including 1,219 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 0.11 ( 1219 hom., cov: 32)

Consequence

LINC00334
NR_135279.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.472
Variant links:
Genes affected
LINC00334 (HGNC:16425): (long intergenic non-protein coding RNA 334)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC00334NR_135279.1 linkuse as main transcriptn.167+964G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC00334ENST00000660971.1 linkuse as main transcriptn.169+994G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16435
AN:
152030
Hom.:
1214
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.191
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.0968
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.143
Gnomad FIN
AF:
0.0492
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.0532
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16472
AN:
152148
Hom.:
1219
Cov.:
32
AF XY:
0.109
AC XY:
8072
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.192
Gnomad4 AMR
AF:
0.0972
Gnomad4 ASJ
AF:
0.133
Gnomad4 EAS
AF:
0.270
Gnomad4 SAS
AF:
0.144
Gnomad4 FIN
AF:
0.0492
Gnomad4 NFE
AF:
0.0532
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.0685
Hom.:
636
Bravo
AF:
0.117
Asia WGS
AF:
0.210
AC:
729
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.56
DANN
Benign
0.46

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2838824; hg19: chr21-46655385; API