rs11568826

Positions:

• chr7-99735355-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The XR_927402.3(ZSCAN25):​n.1456-1337A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 151,732 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.025 (78 hom., cov: 31)
• Consequence: ZSCAN25 XR_927402.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

ZSCAN25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 7-99735355-A-T is Benign according to our data. Variant chr7-99735355-A-T is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0254 (3853/151732) while in subpopulation NFE AF= 0.0341 (2311/67690). AF 95% confidence interval is 0.033. There are 78 homozygotes in gnomad4. There are 1890 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 78 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN25	XR_007059988.1	n.1429-1337A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059989.1	n.1371-1337A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059990.1	n.1244-1337A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_927402.3	n.1456-1337A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3852 AN: 151612 Hom.: 77 Cov.: 31

Gnomad AFR AF: 0.00950

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0281

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0254 AC: 3853 AN: 151732 Hom.: 78 Cov.: 31 AF XY: 0.0255 AC XY: 1890 AN XY: 74180

Gnomad4 AFR AF: 0.00950

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0281

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.0320 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568826; hg19: chr7-99332978;