5-86878330-A-G

Position:

• chr5-86878330-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 0.466 in 152,038 control chromosomes in the GnomAD database, including 17,025 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 0.47 (17025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70846 AN: 151920 Hom.: 17021 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.466 AC: 70861 AN: 152038 Hom.: 17025 Cov.: 32 AF XY: 0.465 AC XY: 34573 AN XY: 74302

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.487

Alfa AF: 0.501 Hom.: 25903

Bravo AF: 0.466

Asia WGS AF: 0.610 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493354; hg19: chr5-86174147;