chr6-38398097-T-C

Variant names:

• chr6-38398097-T-C
• rs9357271
• NM_001099272.2:c.1155-53004A>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.1155-53004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,004 control chromosomes in the GnomAD database, including 13,710 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 0.38 (13710 hom., cov: 32)
• Consequence: BTBD9 NM_001099272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 41 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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.1155-53004A>G		intron	N/A	NP_001092742.1	Q96Q07-1
	BTBD9	NM_052893.2		c.1155-53004A>G		intron	N/A	NP_443125.1	Q96Q07-1
	BTBD9	NM_001172418.2		c.1064+4720A>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.1155-53004A>G		intron	N/A	ENSP00000418751.1	Q96Q07-1
	BTBD9	ENST00000419706.6	TSL:1	c.1064+4720A>G		intron	N/A	ENSP00000415365.2	Q96Q07-2
	BTBD9	ENST00000314100.10	TSL:1	c.951-53004A>G		intron	N/A	ENSP00000323408.6	Q96Q07-3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58222 AN: 151886 Hom.: 13683 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.384 AC: 58295 AN: 152004 Hom.: 13710 Cov.: 32 AF XY: 0.392 AC XY: 29118 AN XY: 74322

African (AFR) AF: 0.585 AC: 24244 AN: 41428

American (AMR) AF: 0.412 AC: 6298 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3472

East Asian (EAS) AF: 0.869 AC: 4491 AN: 5168

South Asian (SAS) AF: 0.496 AC: 2389 AN: 4820

European-Finnish (FIN) AF: 0.346 AC: 3656 AN: 10572

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15170 AN: 67958

Other (OTH) AF: 0.375 AC: 794 AN: 2116

Alfa AF: 0.287 Hom.: 33286

Bravo AF: 0.401

Asia WGS AF: 0.684 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		0.21
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: rs9357271; hg19: chr6-38365873;