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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100Z	XM_011543241.3	c.*3-876C>A		intron_variant	Intron 4 of 4		XP_011541543.1

Ensembl

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

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 v4.3

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;