rs11558476

Variant names:

• chr7-100057066-G-A
• rs11558476
• NM_145914.3:c.60G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-100057066-G-A
• chr7-100057066-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_145914.3(ZSCAN21):​c.60G>A​(p.Gln20Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,613,822 control chromosomes in the GnomAD database, including 74,350 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 0.27 (6422 hom., cov: 32)
  • Exomes 𝑓: 0.30 (67928 hom.)
• Consequence: ZSCAN21 NM_145914.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 24 publications found

Genes affected

ZSCAN21 (HGNC:13104): (zinc finger and SCAN domain containing 21) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP7: Synonymous conserved (PhyloP=-0.403 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145914.3. 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
	ZSCAN21	NM_145914.3	MANE Select	c.60G>A	p.Gln20Gln	synonymous	Exon 2 of 4	NP_666019.1	Q9Y5A6
	ZSCAN21	NM_001362779.2		c.60G>A	p.Gln20Gln	synonymous	Exon 3 of 5	NP_001349708.1	Q9Y5A6
	ZSCAN21	NM_001362780.2		c.60G>A	p.Gln20Gln	synonymous	Exon 3 of 5	NP_001349709.1	Q9Y5A6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN21	ENST00000292450.9	TSL:1 MANE Select	c.60G>A	p.Gln20Gln	synonymous	Exon 2 of 4	ENSP00000292450.4	Q9Y5A6
	ZSCAN21	ENST00000906173.1		c.60G>A	p.Gln20Gln	synonymous	Exon 2 of 4	ENSP00000576232.1
	ZSCAN21	ENST00000906174.1		c.60G>A	p.Gln20Gln	synonymous	Exon 3 of 5	ENSP00000576233.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40887 AN: 151946 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.313

GnomAD2 exomes AF: 0.330 AC: 83049 AN: 251336 AF XY: 0.334

Gnomad AFR exome AF: 0.134

Gnomad AMR exome AF: 0.430

Gnomad ASJ exome AF: 0.376

Gnomad EAS exome AF: 0.486

Gnomad FIN exome AF: 0.286

Gnomad NFE exome AF: 0.286

Gnomad OTH exome AF: 0.346

GnomAD4 exome AF: 0.297 AC: 434816 AN: 1461760 Hom.: 67928 Cov.: 36 AF XY: 0.302 AC XY: 219855 AN XY: 727178

African (AFR) AF: 0.133 AC: 4455 AN: 33476

American (AMR) AF: 0.431 AC: 19274 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 9688 AN: 26136

East Asian (EAS) AF: 0.484 AC: 19220 AN: 39700

South Asian (SAS) AF: 0.404 AC: 34840 AN: 86254

European-Finnish (FIN) AF: 0.285 AC: 15212 AN: 53386

Middle Eastern (MID) AF: 0.500 AC: 2871 AN: 5742

European-Non Finnish (NFE) AF: 0.279 AC: 310104 AN: 1111956

Other (OTH) AF: 0.317 AC: 19152 AN: 60386

GnomAD4 genome AF: 0.269 AC: 40901 AN: 152062 Hom.: 6422 Cov.: 32 AF XY: 0.277 AC XY: 20560 AN XY: 74314

African (AFR) AF: 0.137 AC: 5695 AN: 41534

American (AMR) AF: 0.403 AC: 6155 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2346 AN: 5156

South Asian (SAS) AF: 0.404 AC: 1944 AN: 4816

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19351 AN: 67948

Other (OTH) AF: 0.314 AC: 663 AN: 2110

Alfa AF: 0.293 Hom.: 14530

Bravo AF: 0.274

Asia WGS AF: 0.389 AC: 1351 AN: 3478

EpiCase AF: 0.304

EpiControl AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.7
DANN	Benign	0.67
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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: rs11558476; hg19: chr7-99654689; COSMIC: COSV52850811;