rs6870870

Variant summary

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

The NR_102755.1(IL6ST-DT):​n.388+2946C>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 0.46 in 151,982 control chromosomes in the GnomAD database, including 17,431 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 0.46 ( 17431 hom., cov: 31)

Consequence

IL6ST-DT
NR_102755.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185
Variant links:
Genes affected
IL6ST-DT (HGNC:55804): (IL6ST divergent transcript)

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL6ST-DTNR_102755.1 linkuse as main transcriptn.388+2946C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL6ST-DTENST00000500093.2 linkuse as main transcriptn.388+2946C>A intron_variant, non_coding_transcript_variant 1
ENST00000645512.1 linkuse as main transcriptn.279+4299C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69848
AN:
151864
Hom.:
17393
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.636
Gnomad AMI
AF:
0.476
Gnomad AMR
AF:
0.345
Gnomad ASJ
AF:
0.454
Gnomad EAS
AF:
0.129
Gnomad SAS
AF:
0.349
Gnomad FIN
AF:
0.434
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.416
Gnomad OTH
AF:
0.453
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.460
AC:
69937
AN:
151982
Hom.:
17431
Cov.:
31
AF XY:
0.451
AC XY:
33503
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.637
Gnomad4 AMR
AF:
0.344
Gnomad4 ASJ
AF:
0.454
Gnomad4 EAS
AF:
0.128
Gnomad4 SAS
AF:
0.349
Gnomad4 FIN
AF:
0.434
Gnomad4 NFE
AF:
0.416
Gnomad4 OTH
AF:
0.452
Alfa
AF:
0.421
Hom.:
18701
Bravo
AF:
0.462
Asia WGS
AF:
0.298
AC:
1038
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.89
DANN
Benign
0.62

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: rs6870870; hg19: chr5-55294328; COSMIC: COSV67179184; API