rs12196956

chr6-38175619-G-A

Variant summary

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

The NM_001099272.2(BTBD9):c.1642-437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,194 control chromosomes in the GnomAD database, including 786 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 0.087 (786 hom., cov: 33)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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]

LOC124901315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD9	NM_001099272.2	c.1642-437C>T		intron_variant		ENST00000481247.6
LOC124901315	XR_007059571.1	n.442G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD9	ENST00000481247.6	c.1642-437C>T		intron_variant		5	NM_001099272.2	P1

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13300 AN: 152076 Hom.: 787 Cov.: 33

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0874 AC: 13296 AN: 152194 Hom.: 786 Cov.: 33 AF XY: 0.0891 AC XY: 6629 AN XY: 74406

Gnomad4 AFR AF: 0.0218

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0615

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0935

Alfa AF: 0.109 Hom.: 500

Bravo AF: 0.0765

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.9
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: rs12196956; hg19: chr6-38143395;