chr4-26793981-T-C

Variant names:

• chr4-26793981-T-C
• rs4572866
• XR_001741277.2:n.1833-19700T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741277.2(TBC1D19):​n.1833-19700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,098 control chromosomes in the GnomAD database, including 5,830 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 0.25 (5830 hom., cov: 32)
• Consequence: TBC1D19 XR_001741277.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38015 AN: 151980 Hom.: 5830 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.250 AC: 38001 AN: 152098 Hom.: 5830 Cov.: 32 AF XY: 0.245 AC XY: 18240 AN XY: 74346

African (AFR) AF: 0.0796 AC: 3304 AN: 41532

American (AMR) AF: 0.268 AC: 4091 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3466

East Asian (EAS) AF: 0.0893 AC: 463 AN: 5184

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4822

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10546

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

European-Non Finnish (NFE) AF: 0.345 AC: 23468 AN: 67954

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.314 Hom.: 6645

Bravo AF: 0.245

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4572866; hg19: chr4-26795603;