9-15305380-G-C

Position:

• chr9-15305380-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152574.3(TTC39B):​c.42+1704C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,104 control chromosomes in the GnomAD database, including 41,767 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 0.73 (41767 hom., cov: 32)
• Consequence: TTC39B NM_152574.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

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]

TTC39B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC39B	NM_152574.3	c.42+1704C>G		intron_variant		ENST00000512701.7	NP_689787.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC39B	ENST00000512701.7	c.42+1704C>G		intron_variant		2	NM_152574.3	ENSP00000422496.2

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110604 AN: 151986 Hom.: 41751 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.728 AC: 110658 AN: 152104 Hom.: 41767 Cov.: 32 AF XY: 0.734 AC XY: 54602 AN XY: 74356

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.756

Alfa AF: 0.800 Hom.: 27138

Bravo AF: 0.719

Asia WGS AF: 0.801 AC: 2787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.63

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

Other links and lift over

dbSNP: rs581080; hg19: chr9-15305378;