rs519664

Variant summary

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

The NM_152574.3(TTC39B):​c.78-20642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,144 control chromosomes in the GnomAD database, including 14,383 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 0.36 ( 14383 hom., cov: 33)

Consequence

TTC39B
NM_152574.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.638
Variant links:
Genes affected
TTC39B (HGNC:23704): (tetratricopeptide repeat domain 39B) Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTC39BNM_152574.3 linkuse as main transcriptc.78-20642G>A intron_variant ENST00000512701.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TTC39BENST00000512701.7 linkuse as main transcriptc.78-20642G>A intron_variant 2 NM_152574.3 P1

Frequencies

GnomAD3 genomes
AF:
0.361
AC:
54869
AN:
152026
Hom.:
14331
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.745
Gnomad AMI
AF:
0.265
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.121
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.218
Gnomad FIN
AF:
0.226
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.216
Gnomad OTH
AF:
0.313
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.361
AC:
54981
AN:
152144
Hom.:
14383
Cov.:
33
AF XY:
0.355
AC XY:
26415
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.745
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.121
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.218
Gnomad4 FIN
AF:
0.226
Gnomad4 NFE
AF:
0.216
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.240
Hom.:
7190
Bravo
AF:
0.380
Asia WGS
AF:
0.226
AC:
785
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.71
DANN
Benign
0.50

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: rs519664; hg19: chr9-15246652; COSMIC: COSV52615468; COSMIC: COSV52615468; API