1-22373858-A-G

Variant names:

• chr1-22373858-A-G
• rs34920465

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.436 AC: 18070 AN: 41420

American (AMR) AF: 0.159 AC: 2425 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1113 AN: 5142

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4824

European-Finnish (FIN) AF: 0.0782 AC: 829 AN: 10604

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11676 AN: 67990

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.205 Hom.: 7512

Bravo AF: 0.255

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.50
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs34920465; hg19: chr1-22700351;