rs10483546

Variant summary

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

The NR_039982.1(LINC00639):​n.159+18100G>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 0.144 in 152,142 control chromosomes in the GnomAD database, including 1,901 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 ( 1901 hom., cov: 33)

Consequence

LINC00639
NR_039982.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.197
Variant links:
Genes affected
LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC00639NR_039982.1 linkuse as main transcriptn.159+18100G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC00639ENST00000658492.1 linkuse as main transcriptn.67-33437G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21873
AN:
152024
Hom.:
1894
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.135
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.304
Gnomad ASJ
AF:
0.178
Gnomad EAS
AF:
0.0646
Gnomad SAS
AF:
0.150
Gnomad FIN
AF:
0.119
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.119
Gnomad OTH
AF:
0.181
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21910
AN:
152142
Hom.:
1901
Cov.:
33
AF XY:
0.148
AC XY:
10978
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.136
Gnomad4 AMR
AF:
0.304
Gnomad4 ASJ
AF:
0.178
Gnomad4 EAS
AF:
0.0646
Gnomad4 SAS
AF:
0.151
Gnomad4 FIN
AF:
0.119
Gnomad4 NFE
AF:
0.119
Gnomad4 OTH
AF:
0.182
Alfa
AF:
0.114
Hom.:
730
Bravo
AF:
0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.2
DANN
Benign
0.19

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: rs10483546; hg19: chr14-39341845; API