5-76944022-T-C

Variant names:

• chr5-76944022-T-C
• rs1715749
• XM_011543241.3:c.*3-8813T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011543241.3(S100Z):​c.*3-8813T>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
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.551 AC: 22791 AN: 41344

American (AMR) AF: 0.699 AC: 10660 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3715 AN: 5164

South Asian (SAS) AF: 0.768 AC: 3688 AN: 4802

European-Finnish (FIN) AF: 0.610 AC: 6395 AN: 10484

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44664 AN: 67936

Other (OTH) AF: 0.619 AC: 1305 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1715749; hg19: chr5-76239847;