rs7825794

Variant names:

• chr8-128565240-C-T
• rs7825794

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.257 in 152,016 control chromosomes in the GnomAD database, including 6,981 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 0.26 (6981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38999 AN: 151898 Hom.: 6958 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.257 AC: 39072 AN: 152016 Hom.: 6981 Cov.: 32 AF XY: 0.250 AC XY: 18593 AN XY: 74294

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0476

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.253

Alfa AF: 0.187 Hom.: 4652

Bravo AF: 0.272

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7825794; hg19: chr8-129577486;