6-38393336-C-T

Position:

• chr6-38393336-C-T

Variant summary

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

The NM_001099272.2(BTBD9):​c.1155-48243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,024 control chromosomes in the GnomAD database, including 12,426 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 0.37 (12426 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

Genes affected

BTBD9 (HGNC:21228): (BTB domain containing 9) This locus encodes a BTB/POZ domain-containing protein. This domain is known to be involved in protein-protein interactions. Polymorphisms at this locus have been reported to be associated with susceptibility to Restless Legs Syndrome and may also be associated with Tourette Syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD9	NM_001099272.2	c.1155-48243G>A		intron_variant		ENST00000481247.6	NP_001092742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD9	ENST00000481247.6	c.1155-48243G>A		intron_variant		5	NM_001099272.2	ENSP00000418751	P1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55729 AN: 151906 Hom.: 12396 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.367 AC: 55801 AN: 152024 Hom.: 12426 Cov.: 32 AF XY: 0.376 AC XY: 27925 AN XY: 74312

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.360

Alfa AF: 0.260 Hom.: 12098

Bravo AF: 0.378

Asia WGS AF: 0.670 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.59

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: rs4714156; hg19: chr6-38361112;