rs13219695

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099272.2(BTBD9):​c.1154+39673T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,034 control chromosomes in the GnomAD database, including 2,682 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 0.19 ( 2682 hom., cov: 32)

Consequence

BTBD9
NM_001099272.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.382
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BTBD9NM_001099272.2 linkuse as main transcriptc.1154+39673T>C intron_variant ENST00000481247.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BTBD9ENST00000481247.6 linkuse as main transcriptc.1154+39673T>C intron_variant 5 NM_001099272.2 P1Q96Q07-1

Frequencies

GnomAD3 genomes
AF:
0.186
AC:
28256
AN:
151914
Hom.:
2678
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.195
Gnomad AMI
AF:
0.0746
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.248
Gnomad NFE
AF:
0.171
Gnomad OTH
AF:
0.175
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.186
AC:
28290
AN:
152034
Hom.:
2682
Cov.:
32
AF XY:
0.190
AC XY:
14135
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.196
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.269
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.171
Gnomad4 OTH
AF:
0.177
Alfa
AF:
0.184
Hom.:
586
Bravo
AF:
0.191
Asia WGS
AF:
0.253
AC:
882
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.69
DANN
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13219695; hg19: chr6-38505703; API