rs1998359

Variant summary

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

The NM_001310135.5(TTC6):​c.-16+1201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,168 control chromosomes in the GnomAD database, including 3,381 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 0.20 ( 3381 hom., cov: 32)

Consequence

TTC6
NM_001310135.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.76
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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTC6NM_001310135.5 linkuse as main transcriptc.-16+1201C>G intron_variant ENST00000553443.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TTC6ENST00000553443.6 linkuse as main transcriptc.-16+1201C>G intron_variant 5 NM_001310135.5 P1

Frequencies

GnomAD3 genomes
AF:
0.199
AC:
30283
AN:
152050
Hom.:
3379
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0956
Gnomad AMI
AF:
0.191
Gnomad AMR
AF:
0.199
Gnomad ASJ
AF:
0.265
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.264
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.247
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.199
AC:
30290
AN:
152168
Hom.:
3381
Cov.:
32
AF XY:
0.203
AC XY:
15092
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0955
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.265
Gnomad4 EAS
AF:
0.114
Gnomad4 SAS
AF:
0.265
Gnomad4 FIN
AF:
0.283
Gnomad4 NFE
AF:
0.247
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.123
Hom.:
220
Bravo
AF:
0.186
Asia WGS
AF:
0.169
AC:
590
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.096
DANN
Benign
0.71

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: rs1998359; hg19: chr14-38077148; API