rs11747190

Variant names:

• chr5-76935368-C-A
• rs11747190
• NM_001437779.1:c.*683C>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The NM_001437779.1(S100Z):​c.*683C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,218 control chromosomes in the GnomAD database, including 1,191 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 0.12 (1191 hom., cov: 32)
• Consequence: S100Z NM_001437779.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 3 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100Z	NM_001437779.1	c.*683C>A		3_prime_UTR_variant	Exon 5 of 5		NP_001424708.1
S100Z	NM_001437783.1	c.*683C>A		3_prime_UTR_variant	Exon 3 of 3		NP_001424712.1
S100Z	XM_011543241.3	c.*3-17467C>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: 0.121 AC: 18366 AN: 152100 Hom.: 1185 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.121 AC: 18405 AN: 152218 Hom.: 1191 Cov.: 32 AF XY: 0.118 AC XY: 8771 AN XY: 74416

African (AFR) AF: 0.160 AC: 6667 AN: 41544

American (AMR) AF: 0.111 AC: 1697 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.0464 AC: 240 AN: 5172

South Asian (SAS) AF: 0.0836 AC: 403 AN: 4818

European-Finnish (FIN) AF: 0.0680 AC: 721 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7554 AN: 68008

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.118 Hom.: 1937

Bravo AF: 0.127

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	22
DANN	Benign	0.67
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs11747190; hg19: chr5-76231193;