1-22373858-A-G

Variant names:

• chr1-22373858-A-G
• rs34920465

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 0.24 in 152,034 control chromosomes in the GnomAD database, including 5,624 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 0.24 (5624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.240 AC: 36438 AN: 151914 Hom.: 5606 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.240 AC: 36498 AN: 152034 Hom.: 5624 Cov.: 32 AF XY: 0.232 AC XY: 17265 AN XY: 74326

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.223

Alfa AF: 0.181 Hom.: 827

Bravo AF: 0.255

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34920465; hg19: chr1-22700351;