chr14-37860731-A-T

Variant names:

• chr14-37860731-A-T
• rs8019624
• ENST00000533625.5:n.*1063-13729A>T

Variant summary

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

The ENST00000533625.5(TTC6):​n.*1063-13729A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,146 control chromosomes in the GnomAD database, including 4,660 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 0.14 (4660 hom., cov: 32)
• Consequence: TTC6 ENST00000533625.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC6	ENST00000533625.5	n.*1063-13729A>T		intron_variant	Intron 11 of 18	2		ENSP00000451566.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21579 AN: 152028 Hom.: 4638 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0508

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.142 AC: 21644 AN: 152146 Hom.: 4660 Cov.: 32 AF XY: 0.137 AC XY: 10203 AN XY: 74394

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.0508

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0842 Hom.: 306

Bravo AF: 0.159

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8019624; hg19: chr14-38329936;