9-15305380-G-C

Variant names:

• chr9-15305380-G-C
• rs581080
• NM_152574.3:c.42+1704C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 80 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152574.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC39B	NM_152574.3	MANE Select	c.42+1704C>G		intron	N/A	NP_689787.3
	TTC39B	NM_001168339.2		c.42+1704C>G		intron	N/A	NP_001161811.2
	TTC39B	NM_001168340.2		c.42+1704C>G		intron	N/A	NP_001161812.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC39B	ENST00000512701.7	TSL:2 MANE Select	c.42+1704C>G		intron	N/A	ENSP00000422496.2
	TTC39B	ENST00000506891.1	TSL:1	c.42+1704C>G		intron	N/A	ENSP00000427314.2
	TTC39B	ENST00000505732.5	TSL:1	n.277+1704C>G		intron	N/A

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

African (AFR) AF: 0.499 AC: 20673 AN: 41452

American (AMR) AF: 0.804 AC: 12271 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2660 AN: 3464

East Asian (EAS) AF: 0.907 AC: 4706 AN: 5190

South Asian (SAS) AF: 0.770 AC: 3717 AN: 4826

European-Finnish (FIN) AF: 0.867 AC: 9173 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54991 AN: 68014

Other (OTH) AF: 0.756 AC: 1596 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs581080; hg19: chr9-15305378;