rs7799039

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;