dbSNP rs12132927: S100A7:c.-17-55A>G (chr1-153459085-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002963.4(S100A7):c.-17-55A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 1,582,376 control chromosomes in the GnomAD database, including 6,119 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 0.063 ( 426 hom., cov: 32)

Exomes 𝑓: 0.086 ( 5693 hom. )

Consequence

S100A7
NM_002963.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

7 publications found

Variant links:

Genes affected

S100A7 (HGNC:10497): (S100 calcium binding protein A7) 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 differs from the other S100 proteins of known structure in its lack of calcium binding ability in one EF-hand at the N-terminus. The protein is overexpressed in hyperproliferative skin diseases, exhibits antimicrobial activities against bacteria and induces immunomodulatory activities. [provided by RefSeq, Nov 2014]

S100A7 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A7	NM_002963.4 link	c.-17-55A>G		intron_variant	Intron 1 of 2	ENST00000368723.4	NP_002954.2	P31151

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S100A7	ENST00000368723.4 link	c.-17-55A>G		intron_variant	Intron 1 of 2	1	NM_002963.4	ENSP00000357712.3		P31151
S100A7	ENST00000368722.5 link	c.-17-55A>G		intron_variant	Intron 1 of 2	3		ENSP00000357711.1		P31151

Frequencies

GnomAD3 genomes

AF:

0.0635

AC:

9654

AN:

152098

Hom.:

426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0158

Gnomad AMI

AF:

0.0396

Gnomad AMR

AF:

0.0585

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0818

Gnomad FIN

AF:

0.0647

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0915

Gnomad OTH

AF:

0.0825

GnomAD4 exome

AF:

0.0857

AC:

122600

AN:

1430160

Hom.:

5693

AF XY:

0.0869

AC XY:

61567

AN XY:

708514

show subpopulations

African (AFR)

AF:

0.0143

AC:

467

AN:

32572

American (AMR)

AF:

0.0407

AC:

1706

AN:

41896

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

3627

AN:

24168

East Asian (EAS)

AF:

0.000228

AC:

AN:

39436

South Asian (SAS)

AF:

0.0895

AC:

7253

AN:

81062

European-Finnish (FIN)

AF:

0.0665

AC:

3445

AN:

51770

Middle Eastern (MID)

AF:

0.122

AC:

685

AN:

5606

European-Non Finnish (NFE)

AF:

0.0917

AC:

100364

AN:

1094586

Other (OTH)

AF:

0.0854

AC:

5044

AN:

59064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

5619

11237

16856

22474

28093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3640

7280

10920

14560

18200

<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:

0.0635

AC:

9659

AN:

152216

Hom.:

426

Cov.:

AF XY:

0.0621

AC XY:

4623

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0158

AC:

655

AN:

41552

American (AMR)

AF:

0.0584

AC:

893

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

560

AN:

3466

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0825

AC:

397

AN:

4814

European-Finnish (FIN)

AF:

0.0647

AC:

686

AN:

10602

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0915

AC:

6224

AN:

67996

Other (OTH)

AF:

0.0821

AC:

173

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

455

911

1366

1822

2277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0850

Hom.:

1029

Bravo

AF:

0.0594

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.83

(source)

DANN

Benign

0.66

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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