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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370456	XR_943760.4	n.2814-7057C>A		intron_variant	Intron 1 of 2
LOC105370456	XR_943761.4	n.3061-10942C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC6	ENST00000533625.5	n.*1934-26948G>T		intron_variant	Intron 18 of 18	2		ENSP00000451566.1
TTC6	ENST00000553887.1	n.121-26948G>T		intron_variant	Intron 1 of 1	3

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 v4.3

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

Other links and lift over

dbSNP: rs10498333; hg19: chr14-38483515;