rs3792738

Variant names:

• chr5-76951959-C-A
• rs3792738
• XM_011543241.3:c.*3-876C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-76951959-C-A
• chr5-76951959-C-G
• chr5-76951959-C-T

Variant summary

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

The XM_011543241.3(S100Z):​c.*3-876C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,186 control chromosomes in the GnomAD database, including 510 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 0.079 (510 hom., cov: 33)
• Consequence: S100Z XM_011543241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 11 publications found

Genes affected

S100Z (HGNC:30367): (S100 calcium binding protein Z) Members of the S100 protein family contain 2 calcium-binding EF-hands and exhibit cell-type specific expression patterns. For additional background information on S100 proteins, see MIM 114085.[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11968 AN: 152068 Hom.: 508 Cov.: 33

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0820

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0787 AC: 11974 AN: 152186 Hom.: 510 Cov.: 33 AF XY: 0.0793 AC XY: 5900 AN XY: 74384

African (AFR) AF: 0.0829 AC: 3442 AN: 41536

American (AMR) AF: 0.0805 AC: 1231 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.169 AC: 872 AN: 5166

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4816

European-Finnish (FIN) AF: 0.0820 AC: 868 AN: 10582

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4747 AN: 68002

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0724 Hom.: 761

Bravo AF: 0.0813

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs3792738; hg19: chr5-76247784;