rs7799039

Variant names:

• chr7-128238730-G-A
• rs7799039

Your query was ambiguous. Multiple possible variants found:

• chr7-128238730-G-A
• chr7-128238730-G-C

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 0.366 in 152,070 control chromosomes in the GnomAD database, including 12,642 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 0.37 (12642 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.366 AC: 55641 AN: 151952 Hom.: 12638 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.366 AC: 55647 AN: 152070 Hom.: 12642 Cov.: 33 AF XY: 0.377 AC XY: 28003 AN XY: 74334

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.370

Alfa AF: 0.289 Hom.: 1142

Bravo AF: 0.345

Asia WGS AF: 0.621 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7799039; hg19: chr7-127878783;