dbSNP rs4772: S100A12:c.*40T>C (chr1-153373787-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005621.2(S100A12):c.*40T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,577,288 control chromosomes in the GnomAD database, including 9,497 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 0.10 ( 789 hom., cov: 32)

Exomes 𝑓: 0.11 ( 8708 hom. )

Consequence

S100A12
NM_005621.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

23 publications found

Variant links:

Genes affected

S100A12 (HGNC:10489): (S100 calcium binding protein A12) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein is proposed to be involved in specific calcium-dependent signal transduction pathways and its regulatory effect on cytoskeletal components may modulate various neutrophil activities. The protein includes an antimicrobial peptide which has antibacterial activity. [provided by RefSeq, Nov 2014]

S100A12 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A12	NM_005621.2 link	c.*40T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000368737.5	NP_005612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S100A12	ENST00000368737.5 link	c.*40T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_005621.2	ENSP00000357726.3

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15608

AN:

152080

Hom.:

788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0921

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0965

Gnomad ASJ

AF:

0.0934

Gnomad EAS

AF:

0.0952

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0874

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.105

GnomAD2 exomes

AF:

0.103

AC:

25701

AN:

249376

AF XY:

0.104

show subpopulations

Gnomad AFR exome

AF:

0.0946

Gnomad AMR exome

AF:

0.0897

Gnomad ASJ exome

AF:

0.0987

Gnomad EAS exome

AF:

0.0937

Gnomad FIN exome

AF:

0.0930

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.109

AC:

155403

AN:

1425090

Hom.:

8708

Cov.:

AF XY:

0.109

AC XY:

77711

AN XY:

710862

show subpopulations

African (AFR)

AF:

0.0933

AC:

3047

AN:

32662

American (AMR)

AF:

0.0916

AC:

4053

AN:

44242

Ashkenazi Jewish (ASJ)

AF:

0.0944

AC:

2434

AN:

25784

East Asian (EAS)

AF:

0.0914

AC:

3609

AN:

39498

South Asian (SAS)

AF:

0.105

AC:

8914

AN:

85238

European-Finnish (FIN)

AF:

0.0921

AC:

4916

AN:

53366

Middle Eastern (MID)

AF:

0.102

AC:

579

AN:

5692

European-Non Finnish (NFE)

AF:

0.113

AC:

121480

AN:

1079510

Other (OTH)

AF:

0.108

AC:

6371

AN:

59098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

6508

13016

19525

26033

32541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4384

8768

13152

17536

21920

<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:

0.103

AC:

15616

AN:

152198

Hom.:

789

Cov.:

AF XY:

0.102

AC XY:

7584

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.0920

AC:

3822

AN:

41524

American (AMR)

AF:

0.0965

AC:

1477

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0934

AC:

324

AN:

3470

East Asian (EAS)

AF:

0.0948

AC:

491

AN:

5178

South Asian (SAS)

AF:

0.100

AC:

482

AN:

4818

European-Finnish (FIN)

AF:

0.0874

AC:

927

AN:

10602

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.114

AC:

7732

AN:

67992

Other (OTH)

AF:

0.109

AC:

229

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

719

1437

2156

2874

3593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.107

Hom.:

1482

Bravo

AF:

0.104

Asia WGS

AF:

0.0830

AC:

287

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.40

(source)

DANN

Benign

0.077

PhyloP100

-1.7

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

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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