chr1-166661797-A-G

Variant names:

• chr1-166661797-A-G
• rs577317

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 0.912 in 152,192 control chromosomes in the GnomAD database, including 63,364 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 0.91 (63364 hom., cov: 31)
• Consequence: FMO10P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 1 publications found

Genes affected

FMO10P (HGNC:32211): (flavin containing dimethylaniline monoxygenase 10, pseudogene)

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 = 0.977 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: 0.912 AC: 138718 AN: 152074 Hom.: 63316 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.912 AC: 138825 AN: 152192 Hom.: 63364 Cov.: 31 AF XY: 0.913 AC XY: 67940 AN XY: 74418

African (AFR) AF: 0.888 AC: 36862 AN: 41502

American (AMR) AF: 0.931 AC: 14238 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3268 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5179 AN: 5182

South Asian (SAS) AF: 0.969 AC: 4664 AN: 4812

European-Finnish (FIN) AF: 0.908 AC: 9624 AN: 10604

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61868 AN: 68006

Other (OTH) AF: 0.922 AC: 1950 AN: 2114

Alfa AF: 0.907 Hom.: 8806

Bravo AF: 0.913

Asia WGS AF: 0.974 AC: 3388 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	0.041
DANN	Benign	0.26
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs577317; hg19: chr1-166631034;