6-38515788-T-C

Position:

• chr6-38515788-T-C

Variant summary

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

The NM_001099272.2(BTBD9):​c.1154+61812A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,050 control chromosomes in the GnomAD database, including 7,526 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 0.29 (7526 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD9	NM_001099272.2	c.1154+61812A>G		intron_variant		ENST00000481247.6	NP_001092742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD9	ENST00000481247.6	c.1154+61812A>G		intron_variant		5	NM_001099272.2	ENSP00000418751.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44299 AN: 151932 Hom.: 7524 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.291 AC: 44321 AN: 152050 Hom.: 7526 Cov.: 32 AF XY: 0.301 AC XY: 22374 AN XY: 74322

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.331

Alfa AF: 0.319 Hom.: 5476

Bravo AF: 0.268

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
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: rs6923737; hg19: chr6-38483564;