rs3806232

chr1-153391654-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

S100A8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
S100A8	NM_001319198.2	c.3-1097A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.134

Alfa AF: 0.136 Hom.: 304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806232; hg19: chr1-153364130;