rs10494465

Variant names:

• chr1-166574214-C-T
• rs10494465

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 0.188 in 151,922 control chromosomes in the GnomAD database, including 2,815 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 0.19 (2815 hom., cov: 32)
• Consequence: FMO8P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 5 publications found

Genes affected

FMO8P (HGNC:32209): (flavin containing dimethylaniline monoxygenase 8, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434461.1. You can select a different transcript below to see updated ACMG assignments.

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
	FMO8P	ENST00000434461.1	TSL:6	n.624-386C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28603 AN: 151804 Hom.: 2818 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.188 AC: 28625 AN: 151922 Hom.: 2815 Cov.: 32 AF XY: 0.187 AC XY: 13849 AN XY: 74238

African (AFR) AF: 0.245 AC: 10147 AN: 41424

American (AMR) AF: 0.163 AC: 2486 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.172 AC: 890 AN: 5160

South Asian (SAS) AF: 0.141 AC: 678 AN: 4810

European-Finnish (FIN) AF: 0.157 AC: 1655 AN: 10552

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11554 AN: 67950

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.175 Hom.: 2074

Bravo AF: 0.192

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.58
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10494465; hg19: chr1-166543451;