chr3-145360822-A-G

Position:

• chr3-145360822-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 0.923 in 151,916 control chromosomes in the GnomAD database, including 64,768 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 0.92 (64768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140131 AN: 151798 Hom.: 64712 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.923 AC: 140245 AN: 151916 Hom.: 64768 Cov.: 32 AF XY: 0.923 AC XY: 68503 AN XY: 74240

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.919

Alfa AF: 0.911 Hom.: 12315

Bravo AF: 0.920

Asia WGS AF: 0.932 AC: 3232 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344971; hg19: chr3-145078609;