rs7793280

Variant names:

• chr7-117977865-C-T
• rs7793280

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 0.345 in 152,066 control chromosomes in the GnomAD database, including 10,269 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 0.35 (10269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.346 AC: 52504 AN: 151948 Hom.: 10275 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.345 AC: 52508 AN: 152066 Hom.: 10269 Cov.: 32 AF XY: 0.353 AC XY: 26209 AN XY: 74350

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.328

Alfa AF: 0.413 Hom.: 6057

Bravo AF: 0.314

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7793280; hg19: chr7-117617919;