rs686030

Variant names:

• chr9-15304784-C-A
• rs686030
• NM_152574.3:c.42+2300G>T

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+2300G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 151,992 control chromosomes in the GnomAD database, including 59,328 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 0.88 (59328 hom., cov: 30)
• Consequence: TTC39B NM_152574.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61
• Publications: 45 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC39B	NM_152574.3	MANE Select	c.42+2300G>T		intron	N/A	NP_689787.3	A0A8V8PNE1
	TTC39B	NM_001168339.2		c.42+2300G>T		intron	N/A	NP_001161811.2
	TTC39B	NM_001168340.2		c.42+2300G>T		intron	N/A	NP_001161812.2	A0A8V8NCV2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC39B	ENST00000512701.7	TSL:2 MANE Select	c.42+2300G>T		intron	N/A	ENSP00000422496.2	A0A8V8PNE1
	TTC39B	ENST00000506891.1	TSL:1	c.42+2300G>T		intron	N/A	ENSP00000427314.2	H0YAJ6
	TTC39B	ENST00000505732.5	TSL:1	n.277+2300G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134115 AN: 151874 Hom.: 59282 Cov.: 30

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.883 AC: 134220 AN: 151992 Hom.: 59328 Cov.: 30 AF XY: 0.885 AC XY: 65748 AN XY: 74280

African (AFR) AF: 0.910 AC: 37707 AN: 41432

American (AMR) AF: 0.896 AC: 13655 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2893 AN: 3470

East Asian (EAS) AF: 0.969 AC: 4984 AN: 5144

South Asian (SAS) AF: 0.942 AC: 4540 AN: 4818

European-Finnish (FIN) AF: 0.893 AC: 9442 AN: 10578

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58218 AN: 67984

Other (OTH) AF: 0.883 AC: 1867 AN: 2114

Alfa AF: 0.866 Hom.: 94598

Bravo AF: 0.885

Asia WGS AF: 0.949 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.57
PhyloP100		-2.6
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: rs686030; hg19: chr9-15304782;