Genetic Variant NM_001329958.2: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:

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=-0.87).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
C11orf21	NM_001329958.2 link	c.53+157G>T	intron_variant	Intron 1 of 3	ENST00000381153.8	NP_001316887.1	Q9P2W6
C11orf21	NM_001142946.3 link	c.106+157G>T	intron_variant	Intron 1 of 4		NP_001136418.1	Q9P2W6E9PAM5
C11orf21	NR_138249.2 link	n.259+1283G>T	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C11orf21	ENST00000381153.8 link	c.53+157G>T	intron_variant	Intron 1 of 3	1	NM_001329958.2	ENSP00000370545.4	Q9P2W6
C11orf21	ENST00000456145.2 link	c.106+157G>T	intron_variant	Intron 1 of 4	1		ENSP00000406541.2	E9PAM5
C11orf21	ENST00000470369.1 link	n.274G>T	non_coding_transcript_exon_variant	Exon 1 of 2	5
C11orf21	ENST00000495467.1 link	n.168+1283G>T	intron_variant	Intron 1 of 2	4

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over