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GeneBe

6-42339783-G-C

Variant summary

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

The NM_001395490.1(TRERF1):c.-371+23214C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,962 control chromosomes in the GnomAD database, including 10,717 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 0.35 ( 10717 hom., cov: 32)

Consequence

TRERF1
NM_001395490.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.90
Variant links:
Genes affected
TRERF1 (HGNC:18273): (transcriptional regulating factor 1) This gene encodes a zinc-finger transcriptional regulating protein which interacts with CBP/p300 to regulate the human gene CYP11A1. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRERF1NM_001395490.1 linkuse as main transcriptc.-371+23214C>G intron_variant ENST00000695948.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRERF1ENST00000695948.1 linkuse as main transcriptc.-371+23214C>G intron_variant NM_001395490.1

Frequencies

GnomAD3 genomes
AF:
0.351
AC:
53326
AN:
151844
Hom.:
10725
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.170
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.342
Gnomad ASJ
AF:
0.572
Gnomad EAS
AF:
0.218
Gnomad SAS
AF:
0.385
Gnomad FIN
AF:
0.336
Gnomad MID
AF:
0.602
Gnomad NFE
AF:
0.461
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.351
AC:
53310
AN:
151962
Hom.:
10717
Cov.:
32
AF XY:
0.344
AC XY:
25574
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.169
Gnomad4 AMR
AF:
0.342
Gnomad4 ASJ
AF:
0.572
Gnomad4 EAS
AF:
0.219
Gnomad4 SAS
AF:
0.384
Gnomad4 FIN
AF:
0.336
Gnomad4 NFE
AF:
0.461
Gnomad4 OTH
AF:
0.410
Alfa
AF:
0.321
Hom.:
1140
Bravo
AF:
0.340
Asia WGS
AF:
0.264
AC:
920
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
13
Dann
Benign
0.76

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: rs2025429; hg19: chr6-42307521; API