1-166789500-T-C

Variant names:

• chr1-166789500-T-C
• rs858792

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 0.869 in 152,178 control chromosomes in the GnomAD database, including 57,540 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 0.87 (57540 hom., cov: 32)
• Consequence: FMO11P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 4 publications found

Genes affected

FMO11P (HGNC:32212): (flavin containing dimethylaniline monoxygenase 11, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMO11P		n.166789500T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMO11P	ENST00000424742.1	n.1012-650T>C		intron_variant	Intron 8 of 9	6

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132091 AN: 152060 Hom.: 57486 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.869 AC: 132199 AN: 152178 Hom.: 57540 Cov.: 32 AF XY: 0.865 AC XY: 64319 AN XY: 74376

African (AFR) AF: 0.911 AC: 37833 AN: 41522

American (AMR) AF: 0.883 AC: 13502 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3154 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3930 AN: 5176

South Asian (SAS) AF: 0.763 AC: 3672 AN: 4814

European-Finnish (FIN) AF: 0.805 AC: 8515 AN: 10574

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58623 AN: 68012

Other (OTH) AF: 0.877 AC: 1855 AN: 2116

Alfa AF: 0.871 Hom.: 94636

Bravo AF: 0.881

Asia WGS AF: 0.734 AC: 2552 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	1.2
DANN	Benign	0.38
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs858792; hg19: chr1-166758737;