chr5-140634792-C-T

Variant summary

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

The XM_011537665.3(TMCO6):​c.-129-6873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 150,346 control chromosomes in the GnomAD database, including 31,665 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 ( 31665 hom., cov: 29)

Consequence

TMCO6
XM_011537665.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.34
Variant links:
Genes affected

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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TMCO6XM_011537665.3 linkuse as main transcriptc.-129-6873C>T intron_variant XP_011535967.1
TMCO6XM_024446125.2 linkuse as main transcriptc.-472-4947C>T intron_variant XP_024301893.1
TMCO6XM_047417355.1 linkuse as main transcriptc.-242-4947C>T intron_variant XP_047273311.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.644
AC:
96796
AN:
150224
Hom.:
31602
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.772
Gnomad AMI
AF:
0.250
Gnomad AMR
AF:
0.606
Gnomad ASJ
AF:
0.590
Gnomad EAS
AF:
0.491
Gnomad SAS
AF:
0.523
Gnomad FIN
AF:
0.686
Gnomad MID
AF:
0.615
Gnomad NFE
AF:
0.597
Gnomad OTH
AF:
0.628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.645
AC:
96919
AN:
150346
Hom.:
31665
Cov.:
29
AF XY:
0.644
AC XY:
47330
AN XY:
73452
show subpopulations
Gnomad4 AFR
AF:
0.773
Gnomad4 AMR
AF:
0.606
Gnomad4 ASJ
AF:
0.590
Gnomad4 EAS
AF:
0.492
Gnomad4 SAS
AF:
0.524
Gnomad4 FIN
AF:
0.686
Gnomad4 NFE
AF:
0.597
Gnomad4 OTH
AF:
0.629
Alfa
AF:
0.613
Hom.:
3417
Bravo
AF:
0.636
Asia WGS
AF:
0.585
AC:
2035
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.6
DANN
Benign
0.72

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: rs2915863; hg19: chr5-140014377; COSMIC: COSV52800011; API