rs686030

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC39B	NM_152574.3	c.42+2300G>T		intron_variant	Intron 1 of 19	ENST00000512701.7	NP_689787.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC39B	ENST00000512701.7	c.42+2300G>T		intron_variant	Intron 1 of 19	2	NM_152574.3	ENSP00000422496.2

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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.883

Alfa AF: 0.863 Hom.: 73723

Bravo AF: 0.885

Asia WGS AF: 0.949 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.57

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: rs686030; hg19: chr9-15304782;