rs7825794

Variant names:

• chr8-128565240-C-T
• rs7825794

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.510 AC: 21125 AN: 41398

American (AMR) AF: 0.164 AC: 2501 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.0476 AC: 246 AN: 5168

South Asian (SAS) AF: 0.156 AC: 751 AN: 4816

European-Finnish (FIN) AF: 0.126 AC: 1335 AN: 10584

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11485 AN: 67986

Other (OTH) AF: 0.253 AC: 534 AN: 2110

Alfa AF: 0.194 Hom.: 7014

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7825794; hg19: chr8-129577486;