1-228969398-A-G

Variant names:

• chr1-228969398-A-G
• rs603404

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 0.645 in 151,762 control chromosomes in the GnomAD database, including 32,012 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 0.65 (32012 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97895 AN: 151644 Hom.: 31994 Cov.: 30

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.645 AC: 97957 AN: 151762 Hom.: 32012 Cov.: 30 AF XY: 0.642 AC XY: 47563 AN XY: 74128

African (AFR) AF: 0.595 AC: 24612 AN: 41344

American (AMR) AF: 0.643 AC: 9819 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2066 AN: 5130

South Asian (SAS) AF: 0.564 AC: 2702 AN: 4792

European-Finnish (FIN) AF: 0.667 AC: 7019 AN: 10520

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47147 AN: 67940

Other (OTH) AF: 0.644 AC: 1356 AN: 2104

Alfa AF: 0.675 Hom.: 70723

Bravo AF: 0.642

Asia WGS AF: 0.487 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.43
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs603404; hg19: chr1-229105145;