8-145065750-C-T

Position:

• chr8-145065750-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The ENST00000648531.1(C8orf33):​c.717C>T​(p.Ser239=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00213 in 151,940 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0021 (2 hom., cov: 31)
• Consequence: C8orf33 ENST00000648531.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.67

Genes affected

C8orf33 (HGNC:26104): (chromosome 8 open reading frame 33)

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 8-145065750-C-T is Benign according to our data. Variant chr8-145065750-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659005.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.67 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C8orf33	ENST00000648531.1	c.717C>T	p.Ser239=	synonymous_variant	6/6			ENSP00000497694
C8orf33	ENST00000647640.1	c.*83C>T		3_prime_UTR_variant	7/7			ENSP00000497608
C8orf33	ENST00000647724.1	c.*90C>T		3_prime_UTR_variant	7/7			ENSP00000496962
C8orf33	ENST00000648784.1	c.*90C>T		3_prime_UTR_variant	7/7			ENSP00000497427

Frequencies

GnomAD3 genomes AF: 0.00213 AC: 323 AN: 151828 Hom.: 2 Cov.: 31

Gnomad AFR AF: 0.000267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00459

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0000948

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00241

Gnomad OTH AF: 0.00384

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

GnomAD4 genome AF: 0.00213 AC: 324 AN: 151940 Hom.: 2 Cov.: 31 AF XY: 0.00205 AC XY: 152 AN XY: 74264

Gnomad4 AFR AF: 0.000290

Gnomad4 AMR AF: 0.00458

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.0000948

Gnomad4 NFE AF: 0.00241

Gnomad4 OTH AF: 0.00380

Alfa AF: 0.00193 Hom.: 0

Bravo AF: 0.00231

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

C8orf33: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs140067069; hg19: chr8-146291136;