XM_011543241.3:c.*3-9264G>T

Variant names:

• chr5-76943571-G-T
• rs1700678
• XM_011543241.3:c.*3-9264G>T

Variant summary

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

The XM_011543241.3(S100Z):​c.*3-9264G>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
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.607 AC: 25170 AN: 41458

American (AMR) AF: 0.706 AC: 10792 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2129 AN: 3472

East Asian (EAS) AF: 0.719 AC: 3700 AN: 5144

South Asian (SAS) AF: 0.765 AC: 3687 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6451 AN: 10554

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

European-Non Finnish (NFE) AF: 0.658 AC: 44717 AN: 67968

Other (OTH) AF: 0.635 AC: 1338 AN: 2108

Alfa AF: 0.608 Hom.: 3288

Bravo AF: 0.652

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.49
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1700678; hg19: chr5-76239396;