5-123821728-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 0.734 in 151,984 control chromosomes in the GnomAD database, including 42,171 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 0.73 (42171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.734 AC: 111434 AN: 151868 Hom.: 42108 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.734 AC: 111555 AN: 151984 Hom.: 42171 Cov.: 31 AF XY: 0.742 AC XY: 55065 AN XY: 74234

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.689

Alfa AF: 0.653 Hom.: 35967

Bravo AF: 0.739

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.64
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs257016; hg19: chr5-123157422;