rs12587630

Variant summary

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

The NM_001310135.5(TTC6):​c.-96+1362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,108 control chromosomes in the GnomAD database, including 183 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 0.031 ( 183 hom., cov: 31)

Consequence

TTC6
NM_001310135.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.99
Variant links:
Genes affected
TTC6 (HGNC:19739): (tetratricopeptide repeat domain 6)

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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTC6NM_001310135.5 linkuse as main transcriptc.-96+1362A>G intron_variant ENST00000553443.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TTC6ENST00000553443.6 linkuse as main transcriptc.-96+1362A>G intron_variant 5 NM_001310135.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0306
AC:
4644
AN:
151990
Hom.:
178
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00839
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0849
Gnomad ASJ
AF:
0.00664
Gnomad EAS
AF:
0.166
Gnomad SAS
AF:
0.0197
Gnomad FIN
AF:
0.0273
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0245
Gnomad OTH
AF:
0.0321
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0307
AC:
4665
AN:
152108
Hom.:
183
Cov.:
31
AF XY:
0.0317
AC XY:
2358
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.00836
Gnomad4 AMR
AF:
0.0857
Gnomad4 ASJ
AF:
0.00664
Gnomad4 EAS
AF:
0.167
Gnomad4 SAS
AF:
0.0199
Gnomad4 FIN
AF:
0.0273
Gnomad4 NFE
AF:
0.0245
Gnomad4 OTH
AF:
0.0327
Alfa
AF:
0.0164
Hom.:
3
Bravo
AF:
0.0364
Asia WGS
AF:
0.0950
AC:
331
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
13
DANN
Benign
0.53

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: rs12587630; hg19: chr14-38066575; API