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GeneBe

rs2430561

chr12-68158742-T-Achr12-68158742-T-G

Variant summary

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

The NM_000619.3(IFNG):c.115-483A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151266 control chromosomes in the gnomAD Genomes database, including 10846 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 0.36 ( 10846 hom., cov: 31)

Consequence

IFNG
NM_000619.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IFNGNM_000619.3 linkuse as main transcriptc.115-483A>T intron_variant ENST00000229135.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IFNGENST00000229135.4 linkuse as main transcriptc.115-483A>T intron_variant 1 NM_000619.3 P1
IFNG-AS1ENST00000536914.1 linkuse as main transcriptn.337-75787T>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.362
AC:
54832
AN:
151266
Hom.:
10846
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.509
Gnomad AMR
AF:
0.325
Gnomad ASJ
AF:
0.442
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.386
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.463
Gnomad OTH
AF:
0.395
Alfa
AF:
0.400
Hom.:
1552
Bravo
AF:
0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
1.2
Dann
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs2430561; hg19: chr12-68552522;