Genetic Variant C11orf21:c.53+157G>T (chr11-2301599-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001329958.2(C11orf21):c.53+157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 631,506 control chromosomes in the GnomAD database, including 29,131 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 0.26 ( 6112 hom., cov: 32)

Exomes 𝑓: 0.30 ( 23019 hom. )

Consequence

C11orf21
NM_001329958.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.386

Publications

27 publications found

Variant links:

Genes affected

C11orf21 (HGNC:13231): (chromosome 11 open reading frame 21) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

C11orf21 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329958.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C11orf21	NM_001329958.2	MANE Select	c.53+157G>T	intron	N/A	NP_001316887.1	Q9P2W6
C11orf21	NM_001142946.3		c.106+157G>T	intron	N/A	NP_001136418.1	E9PAM5
C11orf21	NR_138249.2		n.259+1283G>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C11orf21	ENST00000381153.8	TSL:1 MANE Select	c.53+157G>T	intron	N/A	ENSP00000370545.4	Q9P2W6
C11orf21	ENST00000456145.2	TSL:1	c.106+157G>T	intron	N/A	ENSP00000406541.2	E9PAM5
C11orf21	ENST00000856028.1		c.53+157G>T	intron	N/A	ENSP00000526087.1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39973

AN:

151994

Hom.:

6113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.298

AC:

142992

AN:

479392

Hom.:

23019

Cov.:

AF XY:

0.298

AC XY:

73747

AN XY:

247684

show subpopulations

African (AFR)

AF:

0.109

AC:

1362

AN:

12526

American (AMR)

AF:

0.217

AC:

2868

AN:

13190

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

4653

AN:

12574

East Asian (EAS)

AF:

0.132

AC:

3752

AN:

28320

South Asian (SAS)

AF:

0.235

AC:

8651

AN:

36784

European-Finnish (FIN)

AF:

0.229

AC:

6187

AN:

27016

Middle Eastern (MID)

AF:

0.313

AC:

1124

AN:

3592

European-Non Finnish (NFE)

AF:

0.334

AC:

106661

AN:

319188

Other (OTH)

AF:

0.295

AC:

7734

AN:

26202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

4451

8902

13353

17804

22255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1478

2956

4434

5912

7390

<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:

0.263

AC:

39975

AN:

152114

Hom.:

6112

Cov.:

AF XY:

0.257

AC XY:

19095

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.121

AC:

5011

AN:

41492

American (AMR)

AF:

0.282

AC:

4321

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1340

AN:

3470

East Asian (EAS)

AF:

0.150

AC:

778

AN:

5178

South Asian (SAS)

AF:

0.259

AC:

1246

AN:

4814

European-Finnish (FIN)

AF:

0.226

AC:

2398

AN:

10590

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.350

AC:

23786

AN:

67966

Other (OTH)

AF:

0.304

AC:

639

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1431

2861

4292

5722

7153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.322

Hom.:

30548

Bravo

AF:

0.260

Asia WGS

AF:

0.216

AC:

752

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.3

(source)

DANN

Benign

0.62

PhyloP100

0.39

PromoterAI

0.0043

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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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