5-76943571-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100Z	XM_011543241.3	c.*3-9264G>T		intron_variant	Intron 4 of 4		XP_011541543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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 v4.3

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;