rs6869535

Variant names:

• chr5-40597516-G-A
• rs6869535
• ENST00000637375.1:c.222-27935C>T

Variant summary

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

The ENST00000637375.1(TTC33):​c.222-27935C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,150 control chromosomes in the GnomAD database, including 2,799 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 0.19 (2799 hom., cov: 32)
• Consequence: TTC33 ENST00000637375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC33	ENST00000637375.1	c.222-27935C>T		intron_variant	Intron 2 of 2	5		ENSP00000490134.1
TTC33	ENST00000636863.1	c.326+6416C>T		intron_variant	Intron 3 of 3	5		ENSP00000490389.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28354 AN: 152032 Hom.: 2796 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.186 AC: 28368 AN: 152150 Hom.: 2799 Cov.: 32 AF XY: 0.186 AC XY: 13844 AN XY: 74378

African (AFR) AF: 0.227 AC: 9408 AN: 41492

American (AMR) AF: 0.163 AC: 2485 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3466

East Asian (EAS) AF: 0.0607 AC: 314 AN: 5172

South Asian (SAS) AF: 0.171 AC: 827 AN: 4826

European-Finnish (FIN) AF: 0.232 AC: 2456 AN: 10578

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11643 AN: 68004

Other (OTH) AF: 0.172 AC: 363 AN: 2116

Alfa AF: 0.177 Hom.: 7910

Bravo AF: 0.181

Asia WGS AF: 0.130 AC: 454 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	1.6
DANN	Benign	0.71
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6869535; hg19: chr5-40597618;