rs727505

Positions:

• chr7-124822027-G-A

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 0.232 in 151,870 control chromosomes in the GnomAD database, including 4,358 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 0.23 (4358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35290 AN: 151752 Hom.: 4355 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.232 AC: 35308 AN: 151870 Hom.: 4358 Cov.: 32 AF XY: 0.228 AC XY: 16907 AN XY: 74204

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.223

Alfa AF: 0.272 Hom.: 8707

Bravo AF: 0.231

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727505; hg19: chr7-124462081;