rs1925714

chr1-228515588-A-G

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 0.808 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.808 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

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.824

Alfa AF: 0.818 Hom.: 58888

Bravo AF: 0.805

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1925714; hg19: chr1-228703289;