chr1-153391654-T-C

Variant names:

• chr1-153391654-T-C
• rs3806232
• NM_001319198.2:c.3-1097A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001319198.2(S100A8):​c.3-1097A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,138 control chromosomes in the GnomAD database, including 1,902 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 0.15 (1902 hom., cov: 32)
• Consequence: S100A8 NM_001319198.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 13 publications found

Genes affected

S100A8 (HGNC:10498): (S100 calcium binding protein A8) 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 may function in the inhibition of casein kinase and as a cytokine. Altered expression of this protein is associated with the disease cystic fibrosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A8	NM_001319198.2	c.3-1097A>G		intron_variant	Intron 1 of 2		NP_001306127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22285 AN: 152020 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.131

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22341 AN: 152138 Hom.: 1902 Cov.: 32 AF XY: 0.144 AC XY: 10741 AN XY: 74392

African (AFR) AF: 0.242 AC: 10037 AN: 41454

American (AMR) AF: 0.112 AC: 1710 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5174

South Asian (SAS) AF: 0.104 AC: 504 AN: 4828

European-Finnish (FIN) AF: 0.0886 AC: 940 AN: 10608

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7882 AN: 68000

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.139 Hom.: 325

Bravo AF: 0.153

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs3806232; hg19: chr1-153364130;