rs11390146

Variant names:

• chr1-153547779-AC-A
• rs11390146
• NM_002960.2:c.208delG

Your query was ambiguous. Multiple possible variants found:

• chr1-153547779-AC-A
• chr1-153547779-AC-ACC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_002960.2(S100A3):​c.208delG​(p.Val70TrpfsTer83) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,613,914 control chromosomes in the GnomAD database, including 30 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0029 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0050 (30 hom.)
• Consequence: S100A3 NM_002960.2 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 2 publications found

Genes affected

S100A3 (HGNC:10493): (S100 calcium binding protein A3) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein has the highest content of cysteines of all S100 proteins, has a high affinity for Zinc, and is highly expressed in human hair cuticle. The precise function of this protein is unknown. [provided by RefSeq, Jul 2008]

S100A4 (HGNC:10494): (S100 calcium binding protein A4) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein may function in motility, invasion, and tubulin polymerization. Chromosomal rearrangements and altered expression of this gene have been implicated in tumor metastasis. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

ENSG00000306517 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 30 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002960.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	S100A3	NM_002960.2	MANE Select	c.208delG	p.Val70TrpfsTer83	frameshift	Exon 3 of 3	NP_002951.1
	LOC101928034	NR_125947.1		n.169-640delC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	S100A3	ENST00000368713.8	TSL:1 MANE Select	c.208delG	p.Val70TrpfsTer83	frameshift	Exon 3 of 3	ENSP00000357702.3
	S100A3	ENST00000368712.1	TSL:3	c.208delG	p.Val70TrpfsTer83	frameshift	Exon 3 of 3	ENSP00000357701.1
	S100A3	ENST00000873876.1		c.208delG	p.Val70TrpfsTer83	frameshift	Exon 2 of 2	ENSP00000543935.1

Frequencies

GnomAD3 genomes AF: 0.00289 AC: 440 AN: 152008 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00190

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000944

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00289 AC: 726 AN: 251420 AF XY: 0.00293

Gnomad AFR exome AF: 0.000861

Gnomad AMR exome AF: 0.00168

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000554

Gnomad NFE exome AF: 0.00551

Gnomad OTH exome AF: 0.00245

GnomAD4 exome AF: 0.00501 AC: 7329 AN: 1461788 Hom.: 30 Cov.: 31 AF XY: 0.00486 AC XY: 3537 AN XY: 727212

African (AFR) AF: 0.00131 AC: 44 AN: 33480

American (AMR) AF: 0.00204 AC: 91 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86258

European-Finnish (FIN) AF: 0.000842 AC: 45 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5764

European-Non Finnish (NFE) AF: 0.00624 AC: 6942 AN: 1111936

Other (OTH) AF: 0.00339 AC: 205 AN: 60390

GnomAD4 genome AF: 0.00289 AC: 440 AN: 152126 Hom.: 0 Cov.: 32 AF XY: 0.00253 AC XY: 188 AN XY: 74356

African (AFR) AF: 0.00106 AC: 44 AN: 41486

American (AMR) AF: 0.00190 AC: 29 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.000944 AC: 10 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00516 AC: 351 AN: 67982

Other (OTH) AF: 0.00284 AC: 6 AN: 2110

Alfa AF: 0.00115 Hom.: 0

Bravo AF: 0.00327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.4
Mutation Taster		=63/37	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11390146; hg19: chr1-153520255;