1-15992737-A-G

Variant names:

• chr1-15992737-A-G
• rs848307
• ENST00000505954.1:n.530+427A>G

Variant summary

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

The ENST00000505954.1(TBC1D3P6):​n.530+427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,174 control chromosomes in the GnomAD database, including 62,586 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 0.90 (62586 hom., cov: 31)
• Consequence: TBC1D3P6 ENST00000505954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

TBC1D3P6 (HGNC:43568): (TBC1 domain family member 3 pseudogene 6)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBC1D3P6	ENST00000505954.1	n.530+427A>G		intron_variant	Intron 5 of 7	6

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137605 AN: 152056 Hom.: 62529 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.905 AC: 137716 AN: 152174 Hom.: 62586 Cov.: 31 AF XY: 0.900 AC XY: 66933 AN XY: 74378

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.902

Alfa AF: 0.903 Hom.: 53129

Bravo AF: 0.906

Asia WGS AF: 0.825 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs848307; hg19: chr1-16319232;