1-109284631-A-G

Variant names:

• chr1-109284631-A-G
• rs672569

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 0.761 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.761 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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.818

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs672569; hg19: chr1-109827253;