1-166789500-T-C

Position:

• chr1-166789500-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424742.1(FMO11P):​n.1012-650T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 ENST00000424742.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMO11P	ENST00000424742.1	n.1012-650T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.877

Alfa AF: 0.868 Hom.: 74007

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs858792; hg19: chr1-166758737;