chr16-3382884-G-A

Variant names:

• chr16-3382884-G-A
• rs556687010
• NM_001284527.2:c.2062C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001284527.2(ZSCAN32):​c.2062C>T​(p.Leu688Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000568 in 1,584,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000056 (0 hom.)
• Consequence: ZSCAN32 NM_001284527.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.663
• Publications: 0 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.056937873).

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.2062C>T	p.Leu688Phe	missense	Exon 7 of 7	NP_001271456.1	Q9NX65-1
	ZSCAN32	NM_001324346.2		c.1843C>T	p.Leu615Phe	missense	Exon 5 of 5	NP_001311275.1
	ZSCAN32	NM_001324343.2		c.1663C>T	p.Leu555Phe	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.2062C>T	p.Leu688Phe	missense	Exon 7 of 7	ENSP00000380061.4	Q9NX65-1
	ZSCAN32	ENST00000304926.7	TSL:1	c.1426C>T	p.Leu476Phe	missense	Exon 6 of 6	ENSP00000302502.3	Q9NX65-2
	ENSG00000285329	ENST00000575785.2	TSL:4	n.-13+17702G>A		intron	N/A	ENSP00000477472.1	V9GZ69

Frequencies

GnomAD3 genomes AF: 0.0000657 AC: 10 AN: 152208 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000856 AC: 20 AN: 233718 AF XY: 0.0000949

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000294

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000842

Gnomad OTH exome AF: 0.000360

GnomAD4 exome AF: 0.0000558 AC: 80 AN: 1432428 Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 41 AN XY: 709516

African (AFR) AF: 0.0000311 AC: 1 AN: 32188

American (AMR) AF: 0.000446 AC: 18 AN: 40316

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24512

East Asian (EAS) AF: 0.00 AC: 0 AN: 39262

South Asian (SAS) AF: 0.00 AC: 0 AN: 83710

European-Finnish (FIN) AF: 0.0000190 AC: 1 AN: 52654

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5624

European-Non Finnish (NFE) AF: 0.0000502 AC: 55 AN: 1095266

Other (OTH) AF: 0.0000849 AC: 5 AN: 58896

GnomAD4 genome AF: 0.0000657 AC: 10 AN: 152208 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74358

African (AFR) AF: 0.0000483 AC: 2 AN: 41446

American (AMR) AF: 0.000327 AC: 5 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68042

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.0000221 Hom.: 0

Bravo AF: 0.000128

ExAC AF: 0.0000659 AC: 8

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	Benign	0.17
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	9.3
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	T
Eigen	Benign	-0.89
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.000040	N
LIST_S2	Benign	0.16	T
M_CAP	Benign	0.0023	T
MetaRNN	Benign	0.057	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.95	L
PhyloP100		0.66
PrimateAI	Benign	0.22	T
PROVEAN	Benign	-0.86	N
REVEL	Benign	0.065
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.015	D
Vest4		0.076
MVP		0.067
MPC		0.021
ClinPred		0.050	T
GERP RS		0.40
Varity_R		0.086
gMVP		0.012
Mutation Taster		=99/1	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: rs556687010; hg19: chr16-3432884;