1-227966216-A-G

Variant names:

• chr1-227966216-A-G
• rs849898

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 0.292 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.292 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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.317

Alfa AF: 0.375 Hom.: 11137

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs849898; hg19: chr1-228153917;