6-104900830-C-T

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):​n.458+25754G>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 0.221 in 152,128 control chromosomes in the GnomAD database, including 3,771 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 0.22 ( 3771 hom., cov: 32)

Consequence

LIN28B-AS1
ENST00000636951.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.797
Variant links:
Genes affected
LIN28B-AS1 (HGNC:21553): (LIN28B antisense RNA 1)

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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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
LIN28B-AS1ENST00000636951.1 linkuse as main transcriptn.458+25754G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.221
AC:
33557
AN:
152010
Hom.:
3767
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.219
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.239
Gnomad SAS
AF:
0.168
Gnomad FIN
AF:
0.219
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.227
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.221
AC:
33572
AN:
152128
Hom.:
3771
Cov.:
32
AF XY:
0.221
AC XY:
16441
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.221
Gnomad4 AMR
AF:
0.218
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.239
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.219
Gnomad4 NFE
AF:
0.227
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.218
Hom.:
7442
Bravo
AF:
0.222
Asia WGS
AF:
0.175
AC:
609
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.2
DANN
Benign
0.77

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: rs6923490; hg19: chr6-105348705; COSMIC: COSV60262579; API