rs270331

Variant names:

• chr5-179896119-G-A
• rs270331
• NM_015043.4:c.349-1505C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_015043.4(TBC1D9B):​c.349-1505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00452 in 152,306 control chromosomes in the GnomAD database, including 4 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 0.0045 (4 hom., cov: 33)
• Consequence: TBC1D9B NM_015043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 2 publications found

Genes affected

TBC1D9B (HGNC:29097): (TBC1 domain family member 9B) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBC1D9B	NM_015043.4	c.349-1505C>T		intron_variant	Intron 3 of 20	ENST00000355235.8	NP_055858.2
TBC1D9B	NM_198868.3	c.349-1505C>T		intron_variant	Intron 3 of 21		NP_942568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBC1D9B	ENST00000355235.8	c.349-1505C>T		intron_variant	Intron 3 of 20	5	NM_015043.4	ENSP00000347375.3
TBC1D9B	ENST00000356834.7	c.349-1505C>T		intron_variant	Intron 3 of 21	1		ENSP00000349291.3
TBC1D9B	ENST00000630103.1	c.230-1505C>T		intron_variant	Intron 2 of 2	5		ENSP00000486765.1
TBC1D9B	ENST00000522224.3	n.230-1505C>T		intron_variant	Intron 2 of 3	5		ENSP00000429361.1

Frequencies

GnomAD3 genomes AF: 0.00453 AC: 689 AN: 152188 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00452 AC: 688 AN: 152306 Hom.: 4 Cov.: 33 AF XY: 0.00415 AC XY: 309 AN XY: 74470

African (AFR) AF: 0.0159 AC: 659 AN: 41558

American (AMR) AF: 0.00118 AC: 18 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68036

Other (OTH) AF: 0.00284 AC: 6 AN: 2112

Alfa AF: 0.00479 Hom.: 2

Bravo AF: 0.00521

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.63
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs270331; hg19: chr5-179323119;