chr16-3382913-C-T

Variant names:

• chr16-3382913-C-T
• rs201245225
• NM_001284527.2:c.2033G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001284527.2(ZSCAN32):​c.2033G>A​(p.Arg678His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00021 in 1,609,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00022 (0 hom.)
• Consequence: ZSCAN32 NM_001284527.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -4.59
• Publications: 4 publications found

Genes affected

ZSCAN32 (HGNC:20812): (zinc finger and SCAN domain containing 32) Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285329 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.12132838).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284527.2. 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
	ZSCAN32	NM_001284527.2	MANE Select	c.2033G>A	p.Arg678His	missense	Exon 7 of 7	NP_001271456.1	Q9NX65-1
	ZSCAN32	NM_001324346.2		c.1814G>A	p.Arg605His	missense	Exon 5 of 5	NP_001311275.1
	ZSCAN32	NM_001324343.2		c.1634G>A	p.Arg545His	missense	Exon 6 of 6	NP_001311272.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN32	ENST00000396852.9	TSL:1 MANE Select	c.2033G>A	p.Arg678His	missense	Exon 7 of 7	ENSP00000380061.4	Q9NX65-1
	ZSCAN32	ENST00000304926.7	TSL:1	c.1397G>A	p.Arg466His	missense	Exon 6 of 6	ENSP00000302502.3	Q9NX65-2
	ENSG00000285329	ENST00000575785.2	TSL:4	n.-13+17731C>T		intron	N/A	ENSP00000477472.1	V9GZ69

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152152 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000176

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000129 AC: 32 AN: 247838 AF XY: 0.000112

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000187

Gnomad NFE exome AF: 0.000223

Gnomad OTH exome AF: 0.000166

GnomAD4 exome AF: 0.000222 AC: 323 AN: 1457024 Hom.: 0 Cov.: 31 AF XY: 0.000213 AC XY: 154 AN XY: 724440

African (AFR) AF: 0.00 AC: 0 AN: 33284

American (AMR) AF: 0.00 AC: 0 AN: 44048

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25758

East Asian (EAS) AF: 0.00 AC: 0 AN: 39620

South Asian (SAS) AF: 0.0000233 AC: 2 AN: 85754

European-Finnish (FIN) AF: 0.0000563 AC: 3 AN: 53304

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5746

European-Non Finnish (NFE) AF: 0.000280 AC: 311 AN: 1109410

Other (OTH) AF: 0.000116 AC: 7 AN: 60100

GnomAD4 genome AF: 0.0000985 AC: 15 AN: 152270 Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8 AN XY: 74470

African (AFR) AF: 0.0000241 AC: 1 AN: 41556

American (AMR) AF: 0.0000654 AC: 1 AN: 15298

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10624

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

European-Non Finnish (NFE) AF: 0.000176 AC: 12 AN: 68008

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.000212 Hom.: 0

Bravo AF: 0.0000642

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000107 AC: 13

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.56
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	4.2
DANN	Uncertain	1.0
DEOGEN2	Benign	0.028	T
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.65
FATHMM_MKL	Benign	0.000030	N
LIST_S2	Benign	0.14	T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	1.6	L
PhyloP100		-4.6
PrimateAI	Benign	0.19	T
PROVEAN	Benign	-2.0	N
REVEL	Benign	0.071
Sift	Uncertain	0.021	D
Sift4G	Uncertain	0.0080	D
Vest4		0.047
MVP		0.44
MPC		0.022
ClinPred		0.066	T
GERP RS		1.6
Varity_R		0.041
gMVP		0.026
Mutation Taster		=100/0	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: rs201245225; hg19: chr16-3432913;