rs7720899

chr5-124544201-A-G

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 0.919 in 152,190 control chromosomes in the GnomAD database, including 64,440 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 0.92 (64440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 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: 0.919 AC: 139733 AN: 152070 Hom.: 64383 Cov.: 31

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.919 AC: 139851 AN: 152190 Hom.: 64440 Cov.: 31 AF XY: 0.919 AC XY: 68373 AN XY: 74394

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.910

Alfa AF: 0.900 Hom.: 27054

Bravo AF: 0.918

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.39
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7720899; hg19: chr5-123879894;