6-38246669-C-T

Variant names:

• chr6-38246669-C-T
• rs9349061
• NM_001099272.2:c.1562+9740G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001099272.2(BTBD9):​c.1562+9740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 149,536 control chromosomes in the GnomAD database, including 1,243 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 0.11 (1243 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 2 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]

LOC105375045 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD9	NM_001099272.2	c.1562+9740G>A		intron_variant	Intron 9 of 10	ENST00000481247.6	NP_001092742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD9	ENST00000481247.6	c.1562+9740G>A		intron_variant	Intron 9 of 10	5	NM_001099272.2	ENSP00000418751.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 15834 AN: 149468 Hom.: 1246 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.106 AC: 15834 AN: 149536 Hom.: 1243 Cov.: 32 AF XY: 0.112 AC XY: 8186 AN XY: 72832

African (AFR) AF: 0.0822 AC: 3350 AN: 40732

American (AMR) AF: 0.107 AC: 1608 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 331 AN: 3462

East Asian (EAS) AF: 0.476 AC: 2434 AN: 5118

South Asian (SAS) AF: 0.168 AC: 799 AN: 4748

European-Finnish (FIN) AF: 0.133 AC: 1284 AN: 9634

Middle Eastern (MID) AF: 0.123 AC: 35 AN: 284

European-Non Finnish (NFE) AF: 0.0834 AC: 5634 AN: 67526

Other (OTH) AF: 0.115 AC: 239 AN: 2074

Alfa AF: 0.0894 Hom.: 125

Bravo AF: 0.105

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	17
DANN	Benign	0.71
PhyloP100		0.52
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: rs9349061; hg19: chr6-38214445;