1-227966216-A-G

Variant names:

• chr1-227966216-A-G
• rs849898

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 0.292 in 152,180 control chromosomes in the GnomAD database, including 7,726 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 0.29 (7726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44450 AN: 152062 Hom.: 7726 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.292 AC: 44451 AN: 152180 Hom.: 7726 Cov.: 31 AF XY: 0.285 AC XY: 21190 AN XY: 74400

African (AFR) AF: 0.110 AC: 4548 AN: 41532

American (AMR) AF: 0.324 AC: 4958 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3470

East Asian (EAS) AF: 0.0970 AC: 503 AN: 5186

South Asian (SAS) AF: 0.198 AC: 957 AN: 4826

European-Finnish (FIN) AF: 0.314 AC: 3321 AN: 10588

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27719 AN: 67980

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.375 Hom.: 30462

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.55
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs849898; hg19: chr1-228153917;