1-226466551-G-A

Variant names:

• chr1-226466551-G-A
• rs2099380

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 0.0934 in 152,176 control chromosomes in the GnomAD database, including 873 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 0.093 (873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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: 0.0935 AC: 14221 AN: 152058 Hom.: 874 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0934 AC: 14212 AN: 152176 Hom.: 873 Cov.: 32 AF XY: 0.0929 AC XY: 6915 AN XY: 74400

African (AFR) AF: 0.0297 AC: 1232 AN: 41528

American (AMR) AF: 0.0732 AC: 1118 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1469 AN: 5156

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1229 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8206 AN: 67994

Other (OTH) AF: 0.104 AC: 220 AN: 2116

Alfa AF: 0.112 Hom.: 3266

Bravo AF: 0.0880

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.48
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2099380; hg19: chr1-226654252;