chr14-37598943-C-A

Variant names:

• chr14-37598943-C-A
• rs2145146
• NM_001310135.5:c.-96+2935C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001310135.5(TTC6):​c.-96+2935C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.082 (593 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC6	NM_001310135.5	c.-96+2935C>A		intron_variant	Intron 1 of 32	ENST00000553443.6	NP_001297064.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC6	ENST00000553443.6	c.-96+2935C>A		intron_variant	Intron 1 of 32	5	NM_001310135.5	ENSP00000451131.1

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 11264 AN: 137494 Hom.: 577 Cov.: 30

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0951

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0401

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0650

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0821 AC: 11302 AN: 137622 Hom.: 593 Cov.: 30 AF XY: 0.0900 AC XY: 5979 AN XY: 66436

African (AFR) AF: 0.0185 AC: 694 AN: 37474

American (AMR) AF: 0.124 AC: 1696 AN: 13668

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 214 AN: 3284

East Asian (EAS) AF: 0.172 AC: 698 AN: 4048

South Asian (SAS) AF: 0.223 AC: 877 AN: 3932

European-Finnish (FIN) AF: 0.193 AC: 1676 AN: 8704

Middle Eastern (MID) AF: 0.0388 AC: 10 AN: 258

European-Non Finnish (NFE) AF: 0.0820 AC: 5206 AN: 63472

Other (OTH) AF: 0.0777 AC: 150 AN: 1930

Alfa AF: 0.0340 Hom.: 52

Bravo AF: 0.0691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.55
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2145146; hg19: chr14-38068148;