rs721066

Variant names:

• chr5-118792230-A-G
• rs721066

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.230 AC: 9516 AN: 41460

American (AMR) AF: 0.115 AC: 1754 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.136 AC: 703 AN: 5164

South Asian (SAS) AF: 0.146 AC: 701 AN: 4814

European-Finnish (FIN) AF: 0.0542 AC: 575 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0918 AC: 6245 AN: 68016

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.104 Hom.: 529

Bravo AF: 0.145

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs721066; hg19: chr5-118127925;