rs8018889

chr14-37814386-C-T

Variant summary

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

The NM_001310135.5(TTC6):c.4689+1953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,900 control chromosomes in the GnomAD database, including 1,399 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 0.12 (1399 hom., cov: 32)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC6	NM_001310135.5	c.4689+1953C>T		intron_variant		ENST00000553443.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000553443.6	c.4689+1953C>T		intron_variant		5	NM_001310135.5	P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18661 AN: 151782 Hom.: 1396 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0988

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 18696 AN: 151900 Hom.: 1399 Cov.: 32 AF XY: 0.121 AC XY: 8954 AN XY: 74226

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.109

Alfa AF: 0.107 Hom.: 1210

Bravo AF: 0.124

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8018889; hg19: chr14-38283591;