2-45069386-A-G

Variant names:

• chr2-45069386-A-G
• rs868542

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;