rs10498333

chr14-38014310-G-T

Variant summary

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

The XR_943760.4(LOC105370456):n.2814-7057C>A variant causes a intron, non coding transcript 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: LOC105370456 XR_943760.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

Genes affected

LOC105370456 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370456	XR_943760.4	n.2814-7057C>A		intron_variant, non_coding_transcript_variant
LOC105370456	XR_943761.4	n.3061-10942C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000533625.5	c.*1934-26948G>T		intron_variant, NMD_transcript_variant		2
TTC6	ENST00000553887.1	n.121-26948G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.0400

Gnomad4 NFE AF: 0.00694

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0223 Hom.: 280

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498333; hg19: chr14-38483515;