6-38638835-T-C

Variant names:

• chr6-38638835-T-C
• rs1699001
• NM_001099272.2:c.-28+965A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000481247.6(BTBD9):​c.-28+965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,106 control chromosomes in the GnomAD database, including 35,183 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 0.67 (35183 hom., cov: 31)
• Consequence: BTBD9 ENST00000481247.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481247.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD9	NM_001099272.2	MANE Select	c.-28+965A>G		intron	N/A	NP_001092742.1
	BTBD9	NM_052893.2		c.-228+965A>G		intron	N/A	NP_443125.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD9	ENST00000481247.6	TSL:5 MANE Select	c.-28+965A>G		intron	N/A	ENSP00000418751.1
	BTBD9	ENST00000649492.1		c.-228+965A>G		intron	N/A	ENSP00000497066.1
	BTBD9	ENST00000497373.1	TSL:4	c.-168+965A>G		intron	N/A	ENSP00000418201.1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102355 AN: 151988 Hom.: 35149 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.673 AC: 102440 AN: 152106 Hom.: 35183 Cov.: 31 AF XY: 0.668 AC XY: 49672 AN XY: 74344

African (AFR) AF: 0.817 AC: 33957 AN: 41546

American (AMR) AF: 0.664 AC: 10148 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3466

East Asian (EAS) AF: 0.601 AC: 3105 AN: 5166

South Asian (SAS) AF: 0.555 AC: 2674 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5578 AN: 10552

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42949 AN: 67950

Other (OTH) AF: 0.631 AC: 1333 AN: 2112

Alfa AF: 0.636 Hom.: 6626

Bravo AF: 0.685

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-1.5
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: rs1699001; hg19: chr6-38606611;