rs7720899

Variant names:

• chr5-124544201-A-G
• rs7720899

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;