NM_001310135.5:c.4689+1953C>T

Variant names:

• chr14-37814386-C-T
• rs8018889
• NM_001310135.5:c.4689+1953C>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.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
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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.4689+1953C>T		intron	N/A	NP_001297064.2
	TTC6	NM_001368142.2		c.591+1953C>T		intron	N/A	NP_001355071.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC6	ENST00000553443.6	TSL:5 MANE Select	c.4689+1953C>T		intron	N/A	ENSP00000451131.1
	TTC6	ENST00000382320.4	TSL:2	c.831+1953C>T		intron	N/A	ENSP00000371757.4
	TTC6	ENST00000267368.11	TSL:5	c.591+1953C>T		intron	N/A	ENSP00000267368.7

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

African (AFR) AF: 0.205 AC: 8487 AN: 41392

American (AMR) AF: 0.0729 AC: 1111 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5160

South Asian (SAS) AF: 0.130 AC: 625 AN: 4806

European-Finnish (FIN) AF: 0.0971 AC: 1023 AN: 10538

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0988 AC: 6715 AN: 67972

Other (OTH) AF: 0.109 AC: 230 AN: 2108

Alfa AF: 0.108 Hom.: 1820

Bravo AF: 0.124

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.82
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8018889; hg19: chr14-38283591;