1-22302564-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 0.838 in 151,886 control chromosomes in the GnomAD database, including 53,422 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 0.84 (53422 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

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 (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.838 AC: 127149 AN: 151768 Hom.: 53369 Cov.: 29

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.838 AC: 127259 AN: 151886 Hom.: 53422 Cov.: 29 AF XY: 0.840 AC XY: 62324 AN XY: 74208

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.846

Alfa AF: 0.820 Hom.: 70407

Bravo AF: 0.846

Asia WGS AF: 0.888 AC: 3087 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	0.25
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6426746; hg19: chr1-22629057;