5-86306799-G-T

Position:

• chr5-86306799-G-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 0.791 in 152,068 control chromosomes in the GnomAD database, including 49,477 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 0.79 (49477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

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 (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.791 AC: 120183 AN: 151950 Hom.: 49465 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.791 AC: 120238 AN: 152068 Hom.: 49477 Cov.: 31 AF XY: 0.787 AC XY: 58490 AN XY: 74344

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.807

Alfa AF: 0.789 Hom.: 4343

Bravo AF: 0.768

Asia WGS AF: 0.799 AC: 2775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10070239; hg19: chr5-85602617;