1-15990330-A-T

Variant names:

• chr1-15990330-A-T
• rs848305
• ENST00000505954.1:n.121+339A>T

Variant summary

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

The ENST00000505954.1(TBC1D3P6):​n.121+339A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,150 control chromosomes in the GnomAD database, including 62,791 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 0.91 (62791 hom., cov: 31)
• Consequence: TBC1D3P6 ENST00000505954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 6 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=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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

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
	TBC1D3P6	ENST00000505954.1	TSL:6	n.121+339A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137817 AN: 152032 Hom.: 62734 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.907 AC: 137928 AN: 152150 Hom.: 62791 Cov.: 31 AF XY: 0.901 AC XY: 67016 AN XY: 74380

African (AFR) AF: 0.970 AC: 40276 AN: 41522

American (AMR) AF: 0.837 AC: 12786 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3183 AN: 3472

East Asian (EAS) AF: 0.781 AC: 4020 AN: 5144

South Asian (SAS) AF: 0.908 AC: 4385 AN: 4830

European-Finnish (FIN) AF: 0.834 AC: 8845 AN: 10608

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61444 AN: 67972

Other (OTH) AF: 0.904 AC: 1911 AN: 2114

Alfa AF: 0.909 Hom.: 7820

Bravo AF: 0.908

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.63
DANN	Benign	0.19
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs848305; hg19: chr1-16316825; COSMIC: COSV70031850;