5-83925018-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 0.736 in 152,102 control chromosomes in the GnomAD database, including 41,842 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 0.74 (41842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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: 0.736 AC: 111871 AN: 151984 Hom.: 41811 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.736 AC: 111958 AN: 152102 Hom.: 41842 Cov.: 33 AF XY: 0.733 AC XY: 54490 AN XY: 74346

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.745

Alfa AF: 0.781 Hom.: 20196

Bravo AF: 0.723

Asia WGS AF: 0.666 AC: 2313 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.30
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9791160; hg19: chr5-83220837;