rs3800358

chr6-38174228-G-T

Variant summary

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

The NM_001099272.2(BTBD9):c.*757C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,138 control chromosomes in the GnomAD database, including 8,606 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 0.31 (8605 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: BTBD9 NM_001099272.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD9	NM_001099272.2	c.*757C>A		3_prime_UTR_variant	11/11	ENST00000481247.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD9	ENST00000481247.6	c.*757C>A		3_prime_UTR_variant	11/11	5	NM_001099272.2	P1
BTBD9	ENST00000314100.10	c.*757C>A		3_prime_UTR_variant	10/10	1
BTBD9	ENST00000649492.1	c.*757C>A		3_prime_UTR_variant	12/12			P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47724 AN: 152014 Hom.: 8602 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.314 AC: 47733 AN: 152132 Hom.: 8605 Cov.: 33 AF XY: 0.310 AC XY: 23090 AN XY: 74376

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.331

Alfa AF: 0.389 Hom.: 16235

Bravo AF: 0.296

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	4.2
Dann	Benign	0.83

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: rs3800358; hg19: chr6-38142004;