6-38502311-C-T

Position:

• chr6-38502311-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.1154+75289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,132 control chromosomes in the GnomAD database, including 4,778 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 0.23 (4778 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD9	NM_001099272.2	c.1154+75289G>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.1154+75289G>A		intron_variant		5	NM_001099272.2	ENSP00000418751	P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34253 AN: 152014 Hom.: 4775 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.225 AC: 34251 AN: 152132 Hom.: 4778 Cov.: 32 AF XY: 0.233 AC XY: 17295 AN XY: 74336

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.262

Alfa AF: 0.265 Hom.: 5396

Bravo AF: 0.208

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.51

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: rs4236060; hg19: chr6-38470087;