rs3733868

Positions:

• chr5-160062448-C-T

Variant summary

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

The NM_003314.3(TTC1):​c.746-2484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,316 control chromosomes in the GnomAD database, including 316 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 0.056 (316 hom., cov: 33)
• Consequence: TTC1 NM_003314.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

TTC1 (HGNC:12391): (tetratricopeptide repeat domain 1) This gene encodes a protein that belongs to the tetratrico peptide repeat superfamily of proteins. The encoded protein plays a role in protein-protein interactions, and binds to the Galpha subunit of G protein-coupled receptors to activate the Ras signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

PWWP2A (HGNC:29406): (PWWP domain containing 2A) Enables chromatin binding activity and histone binding activity. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC1	NM_003314.3	c.746-2484C>T		intron_variant		ENST00000231238.10
TTC1	NM_001282500.2	c.746-2484C>T		intron_variant
PWWP2A	XM_011534424.4	c.1566+1209G>A		intron_variant
PWWP2A	XR_007058578.1	n.1743+1094G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC1	ENST00000231238.10	c.746-2484C>T		intron_variant		1	NM_003314.3	P1

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8491 AN: 152196 Hom.: 316 Cov.: 33

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0557 AC: 8483 AN: 152316 Hom.: 316 Cov.: 33 AF XY: 0.0585 AC XY: 4353 AN XY: 74472

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0734

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0644 Hom.: 471

Bravo AF: 0.0517

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs3733868; hg19: chr5-159489455;