rs721066

Variant names:

• chr5-118792230-A-G
• rs721066

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 0.134 in 152,140 control chromosomes in the GnomAD database, including 1,734 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 0.13 (1734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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: 0.133 AC: 20285 AN: 152024 Hom.: 1737 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.134 AC: 20317 AN: 152140 Hom.: 1734 Cov.: 32 AF XY: 0.133 AC XY: 9907 AN XY: 74372

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0918

Gnomad4 OTH AF: 0.122

Alfa AF: 0.102 Hom.: 464

Bravo AF: 0.145

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721066; hg19: chr5-118127925;