rs1998359

Positions:

• chr14-37607943-C-G
• chr14-37607943-C-T

Variant summary

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

The NM_001310135.5(TTC6):​c.-16+1201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,168 control chromosomes in the GnomAD database, including 3,381 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 0.20 (3381 hom., cov: 32)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

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.-16+1201C>G		intron_variant		ENST00000553443.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC6	ENST00000553443.6	c.-16+1201C>G		intron_variant		5	NM_001310135.5	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30283 AN: 152050 Hom.: 3379 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.199 AC: 30290 AN: 152168 Hom.: 3381 Cov.: 32 AF XY: 0.203 AC XY: 15092 AN XY: 74390

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.220

Alfa AF: 0.123 Hom.: 220

Bravo AF: 0.186

Asia WGS AF: 0.169 AC: 590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.096
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998359; hg19: chr14-38077148;