5-83925018-A-G

Variant names:

• chr5-83925018-A-G
• rs9791160

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 0.736 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.607 AC: 25195 AN: 41484

American (AMR) AF: 0.729 AC: 11130 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2406 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3223 AN: 5146

South Asian (SAS) AF: 0.650 AC: 3131 AN: 4816

European-Finnish (FIN) AF: 0.821 AC: 8697 AN: 10594

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55636 AN: 68002

Other (OTH) AF: 0.745 AC: 1574 AN: 2114

Alfa AF: 0.775 Hom.: 29828

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs9791160; hg19: chr5-83220837;