rs2145146

chr14-37598943-C-Achr14-37598943-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001310135.5(TTC6):c.-96+2935C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.082 (593 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC6	NM_001310135.5	c.-96+2935C>A		intron_variant		ENST00000553443.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000553443.6	c.-96+2935C>A		intron_variant		5	NM_001310135.5	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 11264 AN: 137494 Hom.: 577 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0951

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0401

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0650

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0821 AC: 11302 AN: 137622 Hom.: 593 Cov.: 30 AF XY: 0.0900 AC XY: 5979 AN XY: 66436

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0392 Hom.: 40

Bravo AF: 0.0691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2145146; hg19: chr14-38068148;