5-40626651-T-C

Variant names:

• chr5-40626651-T-C
• rs11955175
• ENST00000637375.1:c.222-57070A>G

Variant summary

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

The ENST00000637375.1(TTC33):​c.222-57070A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 152,148 control chromosomes in the GnomAD database, including 603 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 0.083 (603 hom., cov: 32)
• Consequence: TTC33 ENST00000637375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 7 publications found

Genes affected

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

LOC105374737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC33	ENST00000637375.1	TSL:5	c.222-57070A>G		intron	N/A	ENSP00000490134.1
	TTC33	ENST00000636863.1	TSL:5	c.222-22615A>G		intron	N/A	ENSP00000490389.1
	TTC33	ENST00000636106.1	TSL:5	c.222-13270A>G		intron	N/A	ENSP00000490018.1

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12694 AN: 152030 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0835 AC: 12702 AN: 152148 Hom.: 603 Cov.: 32 AF XY: 0.0843 AC XY: 6270 AN XY: 74384

African (AFR) AF: 0.116 AC: 4826 AN: 41502

American (AMR) AF: 0.0554 AC: 847 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4820

European-Finnish (FIN) AF: 0.129 AC: 1365 AN: 10586

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5064 AN: 67986

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0714 Hom.: 249

Bravo AF: 0.0783

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.44
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11955175; hg19: chr5-40626753;