2-85536918-G-A

Position:

• chr2-85536918-G-A

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 0.531 in 152,124 control chromosomes in the GnomAD database, including 22,841 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 0.53 (22841 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85536918G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80638 AN: 152006 Hom.: 22806 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.531 AC: 80728 AN: 152124 Hom.: 22841 Cov.: 33 AF XY: 0.527 AC XY: 39160 AN XY: 74356

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.522

Alfa AF: 0.474 Hom.: 8647

Bravo AF: 0.536

Asia WGS AF: 0.441 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755015; hg19: chr2-85764041;