rs1120322

chr5-106688510-A-Cchr5-106688510-A-Gchr5-106688510-A-T

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 0.884 in 151,782 control chromosomes in the GnomAD database, including 59,496 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 0.88 (59496 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.926 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: 0.884 AC: 134016 AN: 151664 Hom.: 59440 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.884 AC: 134132 AN: 151782 Hom.: 59496 Cov.: 31 AF XY: 0.886 AC XY: 65724 AN XY: 74160

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.896

Alfa AF: 0.905 Hom.: 74528

Bravo AF: 0.878

Asia WGS AF: 0.907 AC: 3153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1120322; hg19: chr5-106024211;