chr8-123142035-C-A

Position:

• chr8-123142035-C-A

Variant summary

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

The NM_145647.4(TBC1D31):​c.2641-227C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 151,374 control chromosomes in the GnomAD database, including 622 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 0.080 (622 hom., cov: 28)
• Consequence: TBC1D31 NM_145647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D31	NM_145647.4	c.2641-227C>A		intron_variant		ENST00000287380.6	NP_663622.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D31	ENST00000287380.6	c.2641-227C>A		intron_variant		1	NM_145647.4	ENSP00000287380	P1

Frequencies

GnomAD3 genomes AF: 0.0803 AC: 12150 AN: 151256 Hom.: 618 Cov.: 28

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.0436

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0804 AC: 12169 AN: 151374 Hom.: 622 Cov.: 28 AF XY: 0.0827 AC XY: 6118 AN XY: 73940

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.0864

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.0824

Alfa AF: 0.0198 Hom.: 893

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
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

Other links and lift over

dbSNP: rs6984928; hg19: chr8-124154275;