rs1925714

Variant names:

• chr1-228515588-A-G
• rs1925714

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 0.808 in 152,012 control chromosomes in the GnomAD database, including 49,618 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 0.81 (49618 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.808 AC: 122709 AN: 151894 Hom.: 49591 Cov.: 30

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.808 AC: 122789 AN: 152012 Hom.: 49618 Cov.: 30 AF XY: 0.809 AC XY: 60096 AN XY: 74278

African (AFR) AF: 0.769 AC: 31881 AN: 41432

American (AMR) AF: 0.804 AC: 12284 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4642 AN: 5156

South Asian (SAS) AF: 0.854 AC: 4097 AN: 4800

European-Finnish (FIN) AF: 0.807 AC: 8528 AN: 10564

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55778 AN: 67988

Other (OTH) AF: 0.824 AC: 1741 AN: 2114

Alfa AF: 0.814 Hom.: 93198

Bravo AF: 0.805

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1925714; hg19: chr1-228703289;