5-893100-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1

The NM_004237.4(TRIP13):​c.92+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,581,206 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 1 hom. )

Consequence

TRIP13
NM_004237.4 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.14
Variant links:
Genes affected
TRIP13 (HGNC:12307): (thyroid hormone receptor interactor 13) This gene encodes a protein that interacts with thyroid hormone receptors, also known as hormone-dependent transcription factors. The gene product interacts specifically with the ligand binding domain. This gene is one of several that may play a role in early-stage non-small cell lung cancer. [provided by RefSeq, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 5-893100-A-G is Benign according to our data. Variant chr5-893100-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3659923.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000122 (175/1429246) while in subpopulation AMR AF= 0.000386 (16/41470). AF 95% confidence interval is 0.000241. There are 1 homozygotes in gnomad4_exome. There are 80 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIP13NM_004237.4 linkc.92+10A>G intron_variant Intron 1 of 12 ENST00000166345.8 NP_004228.1 Q15645-1
TRIP13NM_001166260.2 linkc.92+10A>G intron_variant Intron 1 of 8 NP_001159732.1
TRIP13XM_011514163.2 linkc.92+10A>G intron_variant Intron 1 of 13 XP_011512465.1 Q15645-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIP13ENST00000166345.8 linkc.92+10A>G intron_variant Intron 1 of 12 1 NM_004237.4 ENSP00000166345.3 Q15645-1
TRIP13ENST00000512024.5 linkn.207+10A>G intron_variant Intron 1 of 8 1
TRIP13ENST00000508456.1 linkn.66+10A>G intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.000151
AC:
23
AN:
151842
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.000194
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000133
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000151
AC:
29
AN:
191828
Hom.:
0
AF XY:
0.000124
AC XY:
13
AN XY:
105176
show subpopulations
Gnomad AFR exome
AF:
0.0000884
Gnomad AMR exome
AF:
0.000472
Gnomad ASJ exome
AF:
0.000113
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000779
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000128
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000122
AC:
175
AN:
1429246
Hom.:
1
Cov.:
31
AF XY:
0.000113
AC XY:
80
AN XY:
709180
show subpopulations
Gnomad4 AFR exome
AF:
0.0000908
Gnomad4 AMR exome
AF:
0.000386
Gnomad4 ASJ exome
AF:
0.000431
Gnomad4 EAS exome
AF:
0.0000259
Gnomad4 SAS exome
AF:
0.0000972
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000112
Gnomad4 OTH exome
AF:
0.000202
GnomAD4 genome
AF:
0.000151
AC:
23
AN:
151960
Hom.:
0
Cov.:
32
AF XY:
0.000148
AC XY:
11
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.000169
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.000195
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000133
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.000155

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 04, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
2.2
DANN
Benign
0.14
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2

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: rs376619779; hg19: chr5-893215; API