7-25820960-G-T

Variant names:

• chr7-25820960-G-T
• rs7798002

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 0.207 in 152,048 control chromosomes in the GnomAD database, including 3,581 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 0.21 (3581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 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: 0.207 AC: 31378 AN: 151930 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31402 AN: 152048 Hom.: 3581 Cov.: 32 AF XY: 0.214 AC XY: 15933 AN XY: 74296

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.204

Alfa AF: 0.0984 Hom.: 158

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7798002; hg19: chr7-25860580;