2-45069386-A-G

Position:

• chr2-45069386-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 0.761 in 152,046 control chromosomes in the GnomAD database, including 44,178 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 0.76 (44178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

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 (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.761 AC: 115624 AN: 151928 Hom.: 44134 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.761 AC: 115730 AN: 152046 Hom.: 44178 Cov.: 31 AF XY: 0.759 AC XY: 56412 AN XY: 74290

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.757

Alfa AF: 0.750 Hom.: 57088

Bravo AF: 0.764

Asia WGS AF: 0.704 AC: 2450 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	1.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868542; hg19: chr2-45296525;