rs9671863

chr14-37658670-A-G

Variant summary

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

The NM_001310135.5(TTC6):c.940-21481A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,186 control chromosomes in the GnomAD database, including 3,175 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 0.19 (3175 hom., cov: 32)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC6	NM_001310135.5	c.940-21481A>G		intron_variant		ENST00000553443.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000553443.6	c.940-21481A>G		intron_variant		5	NM_001310135.5	P1
TTC6	ENST00000533625.5	c.940-21481A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28551 AN: 152068 Hom.: 3174 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.188 AC: 28551 AN: 152186 Hom.: 3175 Cov.: 32 AF XY: 0.191 AC XY: 14229 AN XY: 74404

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.208

Alfa AF: 0.217 Hom.: 615

Bravo AF: 0.173

Asia WGS AF: 0.163 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.8
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs9671863; hg19: chr14-38127875;