rs177852

Variant names:

• chr14-37642665-C-T
• rs177852
• NM_001310135.5:c.939+19662C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001310135.5(TTC6):​c.939+19662C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,896 control chromosomes in the GnomAD database, including 5,748 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 0.26 (5748 hom., cov: 32)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001310135.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC6	NM_001310135.5	MANE Select	c.939+19662C>T		intron	N/A	NP_001297064.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC6	ENST00000553443.6	TSL:5 MANE Select	c.939+19662C>T		intron	N/A	ENSP00000451131.1
	TTC6	ENST00000533625.5	TSL:2	n.939+19662C>T		intron	N/A	ENSP00000451566.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39608 AN: 151774 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.261 AC: 39618 AN: 151896 Hom.: 5748 Cov.: 32 AF XY: 0.262 AC XY: 19420 AN XY: 74202

African (AFR) AF: 0.136 AC: 5644 AN: 41446

American (AMR) AF: 0.237 AC: 3612 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.117 AC: 600 AN: 5134

South Asian (SAS) AF: 0.320 AC: 1537 AN: 4808

European-Finnish (FIN) AF: 0.344 AC: 3620 AN: 10522

Middle Eastern (MID) AF: 0.266 AC: 77 AN: 290

European-Non Finnish (NFE) AF: 0.333 AC: 22630 AN: 67946

Other (OTH) AF: 0.277 AC: 586 AN: 2112

Alfa AF: 0.309 Hom.: 30989

Bravo AF: 0.244

Asia WGS AF: 0.193 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.31
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs177852; hg19: chr14-38111870;