rs4646457

Variant names:

• chr7-99647457-A-C
• rs4646457
• NM_001350984.2:c.806-21638A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-99647457-A-C
• chr7-99647457-A-G
• chr7-99647457-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350984.2(ZSCAN25):​c.806-21638A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 982,922 control chromosomes in the GnomAD database, including 19,555 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 0.28 (11433 hom., cov: 32)
  • Exomes 𝑓: 0.098 (8122 hom.)
• Consequence: ZSCAN25 NM_001350984.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 24 publications found

Genes affected

ZSCAN25 (HGNC:21961): (zinc finger and SCAN domain containing 25) This gene encodes a protein that bears some similarity to zinc finger proteins, which are involved in DNA binding and protein-protein interactions. Multiple alternatively spliced transcript variants have been identified, but the full-length nature for most of them has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN25	NM_001350984.2	c.806-21638A>C		intron_variant	Intron 7 of 7		NP_001337913.1
ZSCAN25	NM_001350985.2	c.806-21638A>C		intron_variant	Intron 5 of 5		NP_001337914.1
ZSCAN25	XM_011515909.3	c.806-21638A>C		intron_variant	Intron 7 of 7		XP_011514211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42118 AN: 152036 Hom.: 11392 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.0975 AC: 81013 AN: 830768 Hom.: 8122 Cov.: 20 AF XY: 0.0968 AC XY: 37132 AN XY: 383760

African (AFR) AF: 0.754 AC: 11863 AN: 15724

American (AMR) AF: 0.184 AC: 180 AN: 980

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 370 AN: 5136

East Asian (EAS) AF: 0.290 AC: 1047 AN: 3612

South Asian (SAS) AF: 0.270 AC: 4439 AN: 16416

European-Finnish (FIN) AF: 0.0652 AC: 18 AN: 276

Middle Eastern (MID) AF: 0.0927 AC: 150 AN: 1618

European-Non Finnish (NFE) AF: 0.0777 AC: 59072 AN: 759784

Other (OTH) AF: 0.142 AC: 3874 AN: 27222

GnomAD4 genome AF: 0.277 AC: 42214 AN: 152154 Hom.: 11433 Cov.: 32 AF XY: 0.276 AC XY: 20547 AN XY: 74394

African (AFR) AF: 0.698 AC: 28954 AN: 41454

American (AMR) AF: 0.223 AC: 3409 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1511 AN: 5172

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4826

European-Finnish (FIN) AF: 0.0686 AC: 728 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0773 AC: 5260 AN: 68004

Other (OTH) AF: 0.232 AC: 490 AN: 2116

Alfa AF: 0.144 Hom.: 13529

Bravo AF: 0.305

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4646457; hg19: chr7-99245080;