rs7561692

Variant summary

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

The ENST00000658738.1(LINC01121):​n.708+18306A>G 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 0.174 in 152,130 control chromosomes in the GnomAD database, including 2,730 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 0.17 ( 2730 hom., cov: 32)

Consequence

LINC01121
ENST00000658738.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.719
Variant links:
Genes affected
LINC01121 (HGNC:49266): (long intergenic non-protein coding RNA 1121)

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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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
LINC01121ENST00000658738.1 linkuse as main transcriptn.708+18306A>G intron_variant, non_coding_transcript_variant
LINC01121ENST00000427020.6 linkuse as main transcriptn.704+18306A>G intron_variant, non_coding_transcript_variant 3
LINC01121ENST00000430650.2 linkuse as main transcriptn.716+18306A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26398
AN:
152010
Hom.:
2720
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.0970
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.374
Gnomad SAS
AF:
0.142
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.132
Gnomad OTH
AF:
0.155
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.174
AC:
26431
AN:
152130
Hom.:
2730
Cov.:
32
AF XY:
0.174
AC XY:
12947
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.252
Gnomad4 AMR
AF:
0.0968
Gnomad4 ASJ
AF:
0.115
Gnomad4 EAS
AF:
0.374
Gnomad4 SAS
AF:
0.143
Gnomad4 FIN
AF:
0.195
Gnomad4 NFE
AF:
0.132
Gnomad4 OTH
AF:
0.153
Alfa
AF:
0.143
Hom.:
984
Bravo
AF:
0.172
Asia WGS
AF:
0.264
AC:
922
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.66
DANN
Benign
0.72

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: rs7561692; hg19: chr2-45509817; API