Variant rs4772 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
S100A12	NM_005621.2 link	c.*40T>C		3_prime_UTR_variant	3/3	ENST00000368737.5	NP_005612.1	P80511

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
S100A12	ENST00000368737 link	c.*40T>C		3_prime_UTR_variant	3/3	1	NM_005621.2	ENSP00000357726.3		P80511

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

GnomAD3 exomes

AF:

0.103

AC:

25701

AN:

249376

Hom.:

1354

AF XY:

0.104

AC XY:

14005

AN XY:

134906

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 SAS exome

AF:

0.105

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

Gnomad4 AFR exome

AF:

0.0933

Gnomad4 AMR exome

AF:

0.0916

Gnomad4 ASJ exome

AF:

0.0944

Gnomad4 EAS exome

AF:

0.0914

Gnomad4 SAS exome

AF:

0.105

Gnomad4 FIN exome

AF:

0.0921

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.108

GnomAD4 genome

AF:

0.103

AC:

15616

AN:

152198

Hom.:

789

Cov.:

AF XY:

0.102

AC XY:

7584

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0920

Gnomad4 AMR

AF:

0.0965

Gnomad4 ASJ

AF:

0.0934

Gnomad4 EAS

AF:

0.0948

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0874

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.106

Hom.:

1020

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

DANN

Benign

0.077

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over