dbSNP rs17410035: C5orf22:c.870+24G>T (chr5-31541035-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018356.3(C5orf22):c.870+24G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,557,702 control chromosomes in the GnomAD database, including 76,909 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 0.24 ( 5351 hom., cov: 31)

Exomes 𝑓: 0.31 ( 71558 hom. )

Consequence

C5orf22
NM_018356.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.942

Publications

18 publications found

Variant links:

Genes affected

C5orf22 (HGNC:25639): (chromosome 5 open reading frame 22)

C5orf22 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018356.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf22	NM_018356.3	MANE Select	c.870+24G>T		intron	N/A	NP_060826.2	Q49AR2-1
	C5orf22	NR_134298.2		n.738+24G>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C5orf22	ENST00000325366.14	TSL:1 MANE Select	c.870+24G>T	intron	N/A	ENSP00000326879.9	Q49AR2-1
C5orf22	ENST00000510659.5	TSL:1	n.*235+24G>T	intron	N/A	ENSP00000423039.1	B4DR92
C5orf22	ENST00000926221.1		c.324+24G>T	intron	N/A	ENSP00000596280.1

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

36915

AN:

150732

Hom.:

5346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0928

Gnomad AMI

AF:

0.183

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.248

GnomAD2 exomes

AF:

0.276

AC:

67041

AN:

243230

AF XY:

0.286

show subpopulations

Gnomad AFR exome

AF:

0.0896

Gnomad AMR exome

AF:

0.189

Gnomad ASJ exome

AF:

0.317

Gnomad EAS exome

AF:

0.167

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.330

Gnomad OTH exome

AF:

0.288

GnomAD4 exome

AF:

0.311

AC:

437865

AN:

1406858

Hom.:

71558

Cov.:

AF XY:

0.313

AC XY:

220004

AN XY:

702700

show subpopulations

African (AFR)

AF:

0.0820

AC:

2624

AN:

32000

American (AMR)

AF:

0.190

AC:

7971

AN:

41844

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

7955

AN:

25392

East Asian (EAS)

AF:

0.148

AC:

5829

AN:

39352

South Asian (SAS)

AF:

0.325

AC:

27191

AN:

83772

European-Finnish (FIN)

AF:

0.263

AC:

14011

AN:

53240

Middle Eastern (MID)

AF:

0.232

AC:

1303

AN:

5612

European-Non Finnish (NFE)

AF:

0.332

AC:

353845

AN:

1067170

Other (OTH)

AF:

0.293

AC:

17136

AN:

58476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

13131

26262

39393

52524

65655

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11010

22020

33030

44040

55050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.245

AC:

36931

AN:

150844

Hom.:

5351

Cov.:

AF XY:

0.242

AC XY:

17799

AN XY:

73628

show subpopulations

African (AFR)

AF:

0.0926

AC:

3797

AN:

41022

American (AMR)

AF:

0.225

AC:

3414

AN:

15144

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1024

AN:

3460

East Asian (EAS)

AF:

0.151

AC:

776

AN:

5128

South Asian (SAS)

AF:

0.333

AC:

1592

AN:

4784

European-Finnish (FIN)

AF:

0.264

AC:

2705

AN:

10238

Middle Eastern (MID)

AF:

0.216

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.337

AC:

22871

AN:

67770

Other (OTH)

AF:

0.249

AC:

523

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1371

2742

4114

5485

6856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.296

Hom.:

19789

Bravo

AF:

0.230

Asia WGS

AF:

0.212

AC:

743

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.4

(source)

DANN

Benign

0.73

PhyloP100

-0.94

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over