rs3792738

chr5-76951959-C-Achr5-76951959-C-Gchr5-76951959-C-T

Variant summary

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

The XM_011543241.3(S100Z):c.*3-876C>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

Genes affected

S100Z (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
S100Z	XM_011543241.3	c.*3-876C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0829

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0442

Gnomad4 FIN AF: 0.0820

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0723 Hom.: 631

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3792738; hg19: chr5-76247784;