1-15992737-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505954.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D3P6	ENST00000505954.1	TSL:6	n.530+427A>G		intron	N/A

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

African (AFR) AF: 0.969 AC: 40257 AN: 41534

American (AMR) AF: 0.835 AC: 12772 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3168 AN: 3472

East Asian (EAS) AF: 0.784 AC: 4029 AN: 5138

South Asian (SAS) AF: 0.912 AC: 4403 AN: 4826

European-Finnish (FIN) AF: 0.835 AC: 8842 AN: 10592

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61260 AN: 68000

Other (OTH) AF: 0.902 AC: 1906 AN: 2112

Alfa AF: 0.904 Hom.: 63431

Bravo AF: 0.906

Asia WGS AF: 0.825 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.7
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs848307; hg19: chr1-16319232;