rs260960

chr4-26631362-C-T

Variant summary

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

The NM_018317.4(TBC1D19):c.295-5849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,832 control chromosomes in the GnomAD database, including 11,781 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 (11781 hom., cov: 32)
• Consequence: TBC1D19 NM_018317.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

TBC1D19 (HGNC:25624): (TBC1 domain family member 19) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D19	NM_018317.4	c.295-5849C>T		intron_variant		ENST00000264866.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBC1D19	ENST00000264866.9	c.295-5849C>T		intron_variant		1	NM_018317.4	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57195 AN: 151714 Hom.: 11775 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.377 AC: 57196 AN: 151832 Hom.: 11781 Cov.: 32 AF XY: 0.376 AC XY: 27869 AN XY: 74180

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.398

Alfa AF: 0.430 Hom.: 2963

Bravo AF: 0.364

Asia WGS AF: 0.373 AC: 1296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.0
Dann	Benign	0.41

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: rs260960; hg19: chr4-26632984;