rs4572866

Positions:

• chr4-26793981-T-C

Variant summary

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

The XR_001741277.2(TBC1D19):​n.1833-19700T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

TBC1D19 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D19	XR_001741277.2	n.1833-19700T>C		intron_variant, non_coding_transcript_variant
TBC1D19	XR_007057937.1	n.1713+29244T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0893

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.267

Alfa AF: 0.322 Hom.: 5048

Bravo AF: 0.245

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4572866; hg19: chr4-26795603;