chr1-227365216-G-A

Variant names:

• chr1-227365216-G-A
• rs3014267

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 0.693 in 151,896 control chromosomes in the GnomAD database, including 36,628 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 0.69 (36628 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 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: 0.693 AC: 105212 AN: 151778 Hom.: 36582 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.693 AC: 105316 AN: 151896 Hom.: 36628 Cov.: 30 AF XY: 0.699 AC XY: 51876 AN XY: 74232

African (AFR) AF: 0.728 AC: 30141 AN: 41412

American (AMR) AF: 0.719 AC: 10959 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.750 AC: 3868 AN: 5156

South Asian (SAS) AF: 0.667 AC: 3206 AN: 4804

European-Finnish (FIN) AF: 0.751 AC: 7932 AN: 10560

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44759 AN: 67936

Other (OTH) AF: 0.669 AC: 1413 AN: 2112

Alfa AF: 0.669 Hom.: 98833

Bravo AF: 0.696

Asia WGS AF: 0.717 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	7.7
DANN	Benign	0.61
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs3014267; hg19: chr1-227552917;