rs10878774

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-48037G>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 0.644 in 151,998 control chromosomes in the GnomAD database, including 32,279 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 0.64 ( 32279 hom., cov: 30)

Consequence

IFNG-AS1
ENST00000536914.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.299
Variant links:
Genes affected
IFNG-AS1 (HGNC:43910): (IFNG 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=-0.99).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105369818XR_001749193.2 linkuse as main transcriptn.3040+548G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IFNG-AS1ENST00000536914.1 linkuse as main transcriptn.337-48037G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.644
AC:
97783
AN:
151880
Hom.:
32235
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.762
Gnomad AMI
AF:
0.544
Gnomad AMR
AF:
0.666
Gnomad ASJ
AF:
0.628
Gnomad EAS
AF:
0.716
Gnomad SAS
AF:
0.801
Gnomad FIN
AF:
0.505
Gnomad MID
AF:
0.778
Gnomad NFE
AF:
0.573
Gnomad OTH
AF:
0.658
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.644
AC:
97883
AN:
151998
Hom.:
32279
Cov.:
30
AF XY:
0.646
AC XY:
47989
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.762
Gnomad4 AMR
AF:
0.667
Gnomad4 ASJ
AF:
0.628
Gnomad4 EAS
AF:
0.716
Gnomad4 SAS
AF:
0.801
Gnomad4 FIN
AF:
0.505
Gnomad4 NFE
AF:
0.573
Gnomad4 OTH
AF:
0.663
Alfa
AF:
0.606
Hom.:
3599
Bravo
AF:
0.658
Asia WGS
AF:
0.776
AC:
2697
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.1
DANN
Benign
0.73

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: rs10878774; hg19: chr12-68580272; API