rs10498333

Variant names:

• chr14-38014310-G-T
• rs10498333
• ENST00000533625.5:n.*1934-26948G>T

Variant summary

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

The ENST00000533625.5(TTC6):​n.*1934-26948G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,196 control chromosomes in the GnomAD database, including 1,309 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 0.085 (1309 hom., cov: 32)
• Consequence: TTC6 ENST00000533625.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 publications found

Genes affected

TTC6 (HGNC:19739): (tetratricopeptide repeat domain 6)

LOC105370456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533625.5. 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
	TTC6	ENST00000533625.5	TSL:2	n.*1934-26948G>T		intron	N/A	ENSP00000451566.1	G3V435
	TTC6	ENST00000553887.1	TSL:3	n.121-26948G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12866 AN: 152078 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00694

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0848 AC: 12902 AN: 152196 Hom.: 1309 Cov.: 32 AF XY: 0.0846 AC XY: 6297 AN XY: 74408

African (AFR) AF: 0.245 AC: 10180 AN: 41490

American (AMR) AF: 0.0579 AC: 885 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3464

East Asian (EAS) AF: 0.107 AC: 556 AN: 5180

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4822

European-Finnish (FIN) AF: 0.0400 AC: 424 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.00694 AC: 472 AN: 68026

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0306 Hom.: 583

Bravo AF: 0.0964

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.73

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10498333;

hg19: chr14-38483515;