6-38515788-T-C

Variant names:

• chr6-38515788-T-C
• rs6923737
• NM_001099272.2:c.1154+61812A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099272.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD9	NM_001099272.2	MANE Select	c.1154+61812A>G		intron	N/A	NP_001092742.1	Q96Q07-1
	BTBD9	NM_052893.2		c.1154+61812A>G		intron	N/A	NP_443125.1	Q96Q07-1
	BTBD9	NM_001172418.2		c.977+61812A>G		intron	N/A	NP_001165889.1	Q96Q07-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD9	ENST00000481247.6	TSL:5 MANE Select	c.1154+61812A>G		intron	N/A	ENSP00000418751.1	Q96Q07-1
	BTBD9	ENST00000419706.6	TSL:1	c.977+61812A>G		intron	N/A	ENSP00000415365.2	Q96Q07-2
	BTBD9	ENST00000314100.10	TSL:1	c.950+61812A>G		intron	N/A	ENSP00000323408.6	Q96Q07-3

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

African (AFR) AF: 0.135 AC: 5616 AN: 41524

American (AMR) AF: 0.241 AC: 3675 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2775 AN: 5180

South Asian (SAS) AF: 0.444 AC: 2139 AN: 4816

European-Finnish (FIN) AF: 0.480 AC: 5058 AN: 10544

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22536 AN: 67922

Other (OTH) AF: 0.331 AC: 700 AN: 2114

Alfa AF: 0.316 Hom.: 6466

Bravo AF: 0.268

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6923737; hg19: chr6-38483564;