rs1553578

Variant names:

• chr5-40669082-G-A
• rs1553578
• ENST00000637375.1:c.221+77716C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637375.1(TTC33):​c.221+77716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,904 control chromosomes in the GnomAD database, including 11,868 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 0.37 (11868 hom., cov: 31)
• Consequence: TTC33 ENST00000637375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 12 publications found

Genes affected

TTC33 (HGNC:29959): (tetratricopeptide repeat domain 33)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637375.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC33	ENST00000637375.1	TSL:5	c.221+77716C>T		intron	N/A	ENSP00000490134.1	A0A1B0GUJ4
	TTC33	ENST00000636863.1	TSL:5	c.222-65046C>T		intron	N/A	ENSP00000490389.1	A0A1B0GV67
	TTC33	ENST00000636106.1	TSL:5	c.222-55701C>T		intron	N/A	ENSP00000490018.1	A0A1B0GU95

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56232 AN: 151784 Hom.: 11865 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.370 AC: 56244 AN: 151904 Hom.: 11868 Cov.: 31 AF XY: 0.370 AC XY: 27463 AN XY: 74230

African (AFR) AF: 0.172 AC: 7146 AN: 41434

American (AMR) AF: 0.474 AC: 7228 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1191 AN: 3456

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5162

South Asian (SAS) AF: 0.373 AC: 1794 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4633 AN: 10526

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31981 AN: 67944

Other (OTH) AF: 0.358 AC: 753 AN: 2104

Alfa AF: 0.414 Hom.: 7788

Bravo AF: 0.363

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1553578; hg19: chr5-40669184;