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rs13029809

Variant summary

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

The NM_017735.5(TTC27):c.1234-10701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,222 control chromosomes in the GnomAD database, including 1,663 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 0.13 ( 1663 hom., cov: 32)

Consequence

TTC27
NM_017735.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.285
Variant links:
Genes affected
TTC27 (HGNC:25986): (tetratricopeptide repeat domain 27)

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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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTC27NM_017735.5 linkuse as main transcriptc.1234-10701A>G intron_variant ENST00000317907.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TTC27ENST00000317907.9 linkuse as main transcriptc.1234-10701A>G intron_variant 1 NM_017735.5 P1
TTC27ENST00000454690.1 linkuse as main transcriptc.*144-10701A>G intron_variant, NMD_transcript_variant 3
TTC27ENST00000647819.1 linkuse as main transcriptc.*439-10701A>G intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.131
AC:
19881
AN:
152104
Hom.:
1660
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.0871
Gnomad ASJ
AF:
0.157
Gnomad EAS
AF:
0.000960
Gnomad SAS
AF:
0.0782
Gnomad FIN
AF:
0.0829
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.0982
Gnomad OTH
AF:
0.125
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.131
AC:
19909
AN:
152222
Hom.:
1663
Cov.:
32
AF XY:
0.128
AC XY:
9511
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.234
Gnomad4 AMR
AF:
0.0871
Gnomad4 ASJ
AF:
0.157
Gnomad4 EAS
AF:
0.000963
Gnomad4 SAS
AF:
0.0777
Gnomad4 FIN
AF:
0.0829
Gnomad4 NFE
AF:
0.0982
Gnomad4 OTH
AF:
0.123
Alfa
AF:
0.107
Hom.:
285
Bravo
AF:
0.135
Asia WGS
AF:
0.0490
AC:
169
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
1.7
Dann
Benign
0.56

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: rs13029809; hg19: chr2-32948194; API