rs12587630

Positions:

• chr14-37597370-A-G
• chr14-37597370-A-T

Variant summary

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

The NM_001310135.5(TTC6):​c.-96+1362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,108 control chromosomes in the GnomAD database, including 183 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 0.031 (183 hom., cov: 31)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC6	NM_001310135.5	c.-96+1362A>G		intron_variant		ENST00000553443.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000553443.6	c.-96+1362A>G		intron_variant		5	NM_001310135.5	P1

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4644 AN: 151990 Hom.: 178 Cov.: 31

Gnomad AFR AF: 0.00839

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0307 AC: 4665 AN: 152108 Hom.: 183 Cov.: 31 AF XY: 0.0317 AC XY: 2358 AN XY: 74342

Gnomad4 AFR AF: 0.00836

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.00664

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0245

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0164 Hom.: 3

Bravo AF: 0.0364

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12587630; hg19: chr14-38066575;