rs3014267

chr1-227365216-G-A

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 0.693 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.669

Alfa AF: 0.663 Hom.: 43945

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3014267; hg19: chr1-227552917;