5-76944022-T-C

Position:

• chr5-76944022-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011543241.3(S100Z):​c.*3-8813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,770 control chromosomes in the GnomAD database, including 30,789 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 0.63 (30789 hom., cov: 30)
• Consequence: S100Z XM_011543241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
S100Z	XM_011543241.3	c.*3-8813T>C		intron_variant			XP_011541543.1
		n.76944022T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96022 AN: 151652 Hom.: 30769 Cov.: 30

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.633 AC: 96083 AN: 151770 Hom.: 30789 Cov.: 30 AF XY: 0.636 AC XY: 47196 AN XY: 74150

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.619

Alfa AF: 0.636 Hom.: 3684

Bravo AF: 0.634

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1715749; hg19: chr5-76239847;