rs2385165

chr8-123110274-A-Cchr8-123110274-A-Gchr8-123110274-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145647.4(TBC1D31):c.1436+654A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,036 control chromosomes in the GnomAD database, including 5,658 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 0.27 (5658 hom., cov: 32)
• Consequence: TBC1D31 NM_145647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

TBC1D31 (HGNC:30888): (TBC1 domain family member 31) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D31	NM_145647.4	c.1436+654A>C		intron_variant		ENST00000287380.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBC1D31	ENST00000287380.6	c.1436+654A>C		intron_variant		1	NM_145647.4	P1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40939 AN: 151918 Hom.: 5649 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.269 AC: 40967 AN: 152036 Hom.: 5658 Cov.: 32 AF XY: 0.270 AC XY: 20092 AN XY: 74312

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.262

Alfa AF: 0.269 Hom.: 2867

Bravo AF: 0.276

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.4
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs2385165; hg19: chr8-124122514;