chr2-85945151-A-G

Position:

• chr2-85945151-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 0.651 in 152,100 control chromosomes in the GnomAD database, including 33,403 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 0.65 (33403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.651 AC: 98951 AN: 151982 Hom.: 33382 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.651 AC: 99017 AN: 152100 Hom.: 33403 Cov.: 32 AF XY: 0.653 AC XY: 48559 AN XY: 74354

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.671

Alfa AF: 0.717 Hom.: 80165

Bravo AF: 0.644

Asia WGS AF: 0.644 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
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: rs1370699; hg19: chr2-86172274;