chr2-85528234-A-G

Position:

• chr2-85528234-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 0.493 in 151,974 control chromosomes in the GnomAD database, including 19,778 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 0.49 (19778 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85528234A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74844 AN: 151856 Hom.: 19748 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.493 AC: 74930 AN: 151974 Hom.: 19778 Cov.: 32 AF XY: 0.489 AC XY: 36370 AN XY: 74306

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.472

Alfa AF: 0.423 Hom.: 22959

Bravo AF: 0.498

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6739015; hg19: chr2-85755357;