chr7-99647390-T-G

Variant names:

• chr7-99647390-T-G
• rs4646458
• NM_001350984.2:c.806-21705T>G

Variant summary

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

The NM_001350984.2(ZSCAN25):​c.806-21705T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 691,652 control chromosomes in the GnomAD database, including 5,717 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 0.15 (3928 hom., cov: 32)
  • Exomes 𝑓: 0.040 (1789 hom.)
• Consequence: ZSCAN25 NM_001350984.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 11 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN25	NM_001350984.2	c.806-21705T>G		intron_variant	Intron 7 of 7		NP_001337913.1
ZSCAN25	NM_001350985.2	c.806-21705T>G		intron_variant	Intron 5 of 5		NP_001337914.1
ZSCAN25	XM_011515909.3	c.806-21705T>G		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: 0.154 AC: 23388 AN: 151932 Hom.: 3912 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.0402 AC: 21713 AN: 539600 Hom.: 1789 AF XY: 0.0397 AC XY: 10056 AN XY: 253276

African (AFR) AF: 0.449 AC: 4860 AN: 10828

American (AMR) AF: 0.119 AC: 75 AN: 632

Ashkenazi Jewish (ASJ) AF: 0.0304 AC: 100 AN: 3294

East Asian (EAS) AF: 0.273 AC: 653 AN: 2392

South Asian (SAS) AF: 0.238 AC: 2565 AN: 10790

European-Finnish (FIN) AF: 0.00556 AC: 1 AN: 180

Middle Eastern (MID) AF: 0.0648 AC: 69 AN: 1064

European-Non Finnish (NFE) AF: 0.0243 AC: 11994 AN: 492800

Other (OTH) AF: 0.0792 AC: 1396 AN: 17620

GnomAD4 genome AF: 0.154 AC: 23448 AN: 152052 Hom.: 3928 Cov.: 32 AF XY: 0.157 AC XY: 11635 AN XY: 74332

African (AFR) AF: 0.399 AC: 16534 AN: 41424

American (AMR) AF: 0.134 AC: 2045 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1381 AN: 5182

South Asian (SAS) AF: 0.258 AC: 1242 AN: 4818

European-Finnish (FIN) AF: 0.0145 AC: 153 AN: 10560

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1649 AN: 67994

Other (OTH) AF: 0.133 AC: 280 AN: 2110

Alfa AF: 0.0720 Hom.: 4141

Bravo AF: 0.169

Asia WGS AF: 0.272 AC: 945 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	0.097
DANN	Benign	0.47
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4646458; hg19: chr7-99245013;