chr5-84920196-T-C

Position:

• chr5-84920196-T-C

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 0.862 in 152,218 control chromosomes in the GnomAD database, including 56,685 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 0.86 (56685 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84920196T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.861 AC: 131031 AN: 152100 Hom.: 56638 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.862 AC: 131137 AN: 152218 Hom.: 56685 Cov.: 32 AF XY: 0.858 AC XY: 63823 AN XY: 74404

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.859

Alfa AF: 0.854 Hom.: 8941

Bravo AF: 0.871

Asia WGS AF: 0.790 AC: 2750 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	0.36
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605987; hg19: chr5-84216014;