Genetic Variant C7orf33:p.Met1? (chr7-148590928-G-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PVS1_SupportingBA1

The NM_145304.4(C7orf33):c.3G>T(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 1,613,828 control chromosomes in the GnomAD database, including 1,328 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 0.031 ( 122 hom., cov: 32)

Exomes 𝑓: 0.037 ( 1206 hom. )

Consequence

C7orf33
NM_145304.4 start_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.652

Variant links:

Genes affected

C7orf33 (HGNC:21724): (chromosome 7 open reading frame 33)

C7orf33 links:

ENSG00000287636 (HGNC:):

ENSG00000287636 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PVS1

Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 76 codons. Genomic position: 148614063. Lost 0.423 part of the original CDS.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C7orf33	NM_145304.4 link	c.3G>T	p.Met1?	start_lost	Exon 1 of 3	ENST00000307003.3	NP_660347.1	Q8WU49A0A090N8Y1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
C7orf33	ENST00000307003.3 link	c.3G>T	p.Met1?	start_lost	Exon 1 of 3	1	NM_145304.4	ENSP00000304071.2	Q8WU49
ENSG00000287636	ENST00000660070.1 link	n.122-4588C>A		intron_variant	Intron 1 of 1
ENSG00000287636	ENST00000686491.1 link	n.250-2893C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0310

AC:

4716

AN:

152102

Hom.:

121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0107

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0863

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0450

Gnomad FIN

AF:

0.0145

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0341

Gnomad OTH

AF:

0.0292

GnomAD3 exomes

AF:

0.0420

AC:

10546

AN:

251364

Hom.:

341

AF XY:

0.0412

AC XY:

5596

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.0108

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.0414

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0511

Gnomad FIN exome

AF:

0.0160

Gnomad NFE exome

AF:

0.0349

Gnomad OTH exome

AF:

0.0434

GnomAD4 exome

AF:

0.0367

AC:

53642

AN:

1461608

Hom.:

1206

Cov.:

AF XY:

0.0369

AC XY:

26858

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.00956

Gnomad4 AMR exome

AF:

0.109

Gnomad4 ASJ exome

AF:

0.0425

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0508

Gnomad4 FIN exome

AF:

0.0159

Gnomad4 NFE exome

AF:

0.0358

Gnomad4 OTH exome

AF:

0.0336

GnomAD4 genome

AF:

0.0310

AC:

4724

AN:

152220

Hom.:

122

Cov.:

AF XY:

0.0313

AC XY:

2332

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0108

Gnomad4 AMR

AF:

0.0863

Gnomad4 ASJ

AF:

0.0397

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.0455

Gnomad4 FIN

AF:

0.0145

Gnomad4 NFE

AF:

0.0341

Gnomad4 OTH

AF:

0.0289

Alfa

AF:

0.0343

Hom.:

174

Bravo

AF:

0.0350

TwinsUK

AF:

0.0356

AC:

132

ALSPAC

AF:

0.0402

AC:

155

ESP6500AA

AF:

0.0123

AC:

ESP6500EA

AF:

0.0338

AC:

291

ExAC

AF:

0.0390

AC:

4738

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0327

EpiControl

AF:

0.0340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.64

CADD

Benign

7.8

DANN

Benign

0.62

DEOGEN2

Benign

0.056

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.014

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.0029

MetaSVM

Benign

-1.1

PROVEAN

Uncertain

-3.6

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Polyphen

0.0050

Vest4

0.072

MutPred

0.83

Gain of catalytic residue at M1 (P = 0.0523);

ClinPred

0.014

GERP RS

-3.8

Varity_R

0.45

gMVP

0.052

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over