rs4434423

Variant names:

• chr5-40677580-T-A
• rs4434423
• ENST00000637375.1:c.221+69218A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-40677580-T-A
• chr5-40677580-T-C

Variant summary

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

The ENST00000637375.1(TTC33):​c.221+69218A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,978 control chromosomes in the GnomAD database, including 29,961 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 0.63 (29961 hom., cov: 31)
• Consequence: TTC33 ENST00000637375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.66 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+69218A>T		intron	N/A	ENSP00000490134.1
	TTC33	ENST00000636863.1	TSL:5	c.221+69218A>T		intron	N/A	ENSP00000490389.1
	TTC33	ENST00000636106.1	TSL:5	c.222-64199A>T		intron	N/A	ENSP00000490018.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95177 AN: 151860 Hom.: 29930 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.627 AC: 95264 AN: 151978 Hom.: 29961 Cov.: 31 AF XY: 0.625 AC XY: 46392 AN XY: 74278

African (AFR) AF: 0.647 AC: 26836 AN: 41460

American (AMR) AF: 0.671 AC: 10242 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3464

East Asian (EAS) AF: 0.498 AC: 2569 AN: 5160

South Asian (SAS) AF: 0.533 AC: 2569 AN: 4816

European-Finnish (FIN) AF: 0.609 AC: 6421 AN: 10542

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42819 AN: 67966

Other (OTH) AF: 0.601 AC: 1267 AN: 2108

Alfa AF: 0.635 Hom.: 3730

Bravo AF: 0.632

Asia WGS AF: 0.546 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs4434423; hg19: chr5-40677682;