Menu
GeneBe

rs6920220

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+11243G>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 0.158 in 151934 control chromosomes in the gnomAD Genomes database, including 2102 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 0.16 ( 2102 hom., cov: 32)

Consequence

LINC03004
ENST00000635999.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14

Links

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=-0.78).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC03004ENST00000635999.1 linkuse as main transcriptn.433+11243G>A intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000638039.1 linkuse as main transcriptn.439-1727G>A intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000646621.1 linkuse as main transcriptn.415-1727G>A intron_variant, non_coding_transcript_variant
LINC03004ENST00000666119.1 linkuse as main transcriptn.393-1727G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.158
AC:
24038
AN:
151934
Hom.:
2102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.158
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.147
Gnomad EAS
AF:
0.00308
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.162
Alfa
AF:
0.190
Hom.:
5602
Bravo
AF:
0.152
Asia WGS
AF:
0.0520
AC:
184
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
6.9
Dann
Benign
0.67

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: rs6920220; hg19: chr6-138006504; API