5-76943571-G-T

Position:

• chr5-76943571-G-T

Variant summary

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

The XM_011543241.3(S100Z):​c.*3-9264G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,018 control chromosomes in the GnomAD database, including 32,277 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 0.65 (32277 hom., cov: 32)
• Consequence: S100Z XM_011543241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
S100Z	XM_011543241.3	c.*3-9264G>T		intron_variant			XP_011541543.1
		n.76943571G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98646 AN: 151900 Hom.: 32248 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.649 AC: 98721 AN: 152018 Hom.: 32277 Cov.: 32 AF XY: 0.652 AC XY: 48439 AN XY: 74306

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.635

Alfa AF: 0.610 Hom.: 3168

Bravo AF: 0.652

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1700678; hg19: chr5-76239396;