1-109284631-A-G

Variant names:

• chr1-109284631-A-G
• rs672569

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 0.761 in 152,106 control chromosomes in the GnomAD database, including 45,840 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 0.76 (45840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.761 AC: 115631 AN: 151988 Hom.: 45823 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.761 AC: 115685 AN: 152106 Hom.: 45840 Cov.: 32 AF XY: 0.765 AC XY: 56891 AN XY: 74382

African (AFR) AF: 0.526 AC: 21780 AN: 41438

American (AMR) AF: 0.885 AC: 13538 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.963 AC: 4975 AN: 5166

South Asian (SAS) AF: 0.920 AC: 4443 AN: 4830

European-Finnish (FIN) AF: 0.826 AC: 8743 AN: 10588

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56581 AN: 67998

Other (OTH) AF: 0.818 AC: 1722 AN: 2106

Alfa AF: 0.777 Hom.: 5844

Bravo AF: 0.753

Asia WGS AF: 0.904 AC: 3143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs672569; hg19: chr1-109827253;