chr7-99735377-A-T

Position:

• chr7-99735377-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.1456-1315A>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 0.0247 in 151,524 control chromosomes in the GnomAD database, including 74 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 (74 hom., cov: 31)
• Consequence: ZSCAN25 XR_927402.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

Genes affected

ZSCAN25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 7-99735377-A-T is Benign according to our data. Variant chr7-99735377-A-T is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0247 (3740/151524) while in subpopulation NFE AF= 0.0332 (2246/67572). AF 95% confidence interval is 0.0321. There are 74 homozygotes in gnomad4. There are 1822 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 74 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN25	XR_007059988.1	n.1429-1315A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059989.1	n.1371-1315A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059990.1	n.1244-1315A>T		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_927402.3	n.1456-1315A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0247 AC: 3739 AN: 151408 Hom.: 73 Cov.: 31

Gnomad AFR AF: 0.00914

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0278

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0123

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0247 AC: 3740 AN: 151524 Hom.: 74 Cov.: 31 AF XY: 0.0246 AC XY: 1822 AN XY: 74038

Gnomad4 AFR AF: 0.00914

Gnomad4 AMR AF: 0.0267

Gnomad4 ASJ AF: 0.0278

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0276

Alfa AF: 0.0298 Hom.: 13

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45494802; hg19: chr7-99333000;