rs4711546

chr6-38398410-A-Gchr6-38398410-A-T

Variant summary

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

The NM_001099272.2(BTBD9):c.1155-53317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,964 control chromosomes in the GnomAD database, including 15,967 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 0.41 (15967 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD9	NM_001099272.2	c.1155-53317T>C		intron_variant		ENST00000481247.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD9	ENST00000481247.6	c.1155-53317T>C		intron_variant		5	NM_001099272.2	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62200 AN: 151846 Hom.: 15934 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.410 AC: 62286 AN: 151964 Hom.: 15967 Cov.: 32 AF XY: 0.419 AC XY: 31091 AN XY: 74272

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.396

Alfa AF: 0.275 Hom.: 13934

Bravo AF: 0.428

Asia WGS AF: 0.759 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	10
Dann	Benign	0.82

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: rs4711546; hg19: chr6-38366186;