chr6-38502311-C-T

Variant names:

• chr6-38502311-C-T
• rs4236060
• NM_001099272.2:c.1154+75289G>A

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+75289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,132 control chromosomes in the GnomAD database, including 4,778 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 0.23 (4778 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 6 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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD9	NM_001099272.2	c.1154+75289G>A		intron_variant	Intron 6 of 10	ENST00000481247.6	NP_001092742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD9	ENST00000481247.6	c.1154+75289G>A		intron_variant	Intron 6 of 10	5	NM_001099272.2	ENSP00000418751.1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34253 AN: 152014 Hom.: 4775 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.225 AC: 34251 AN: 152132 Hom.: 4778 Cov.: 32 AF XY: 0.233 AC XY: 17295 AN XY: 74336

African (AFR) AF: 0.0584 AC: 2427 AN: 41528

American (AMR) AF: 0.220 AC: 3364 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3472

East Asian (EAS) AF: 0.391 AC: 2029 AN: 5186

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4822

European-Finnish (FIN) AF: 0.375 AC: 3954 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18739 AN: 67980

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.257 Hom.: 6702

Bravo AF: 0.208

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.51
PhyloP100		0.43
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: rs4236060; hg19: chr6-38470087;