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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374737	XR_925942.3	n.219+2383T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC33	ENST00000637375.1	c.222-57070A>G		intron_variant	Intron 2 of 2	5		ENSP00000490134.1
TTC33	ENST00000636863.1	c.222-22615A>G		intron_variant	Intron 2 of 3	5		ENSP00000490389.1
TTC33	ENST00000636106.1	c.222-13270A>G		intron_variant	Intron 2 of 2	5		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 v4.3

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;