rs7885012

Variant names:

• chr1-171158257-A-G
• rs7885012
• ENST00000236166.5:n.1257-2797A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000236166.5(FMO6P):​n.1257-2797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,198 control chromosomes in the GnomAD database, including 3,780 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 0.21 (3780 hom., cov: 33)
• Consequence: FMO6P ENST00000236166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 3 publications found

Genes affected

FMO6P (HGNC:24024): (flavin containing dimethylaniline monoxygenase 6, pseudogene) Predicted to enable monooxygenase activity. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FMO6P (HGNC:):

ENSG00000231424 (HGNC:40240):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMO6P	NR_002601.1	n.1720-2901A>G		intron_variant	Intron 6 of 6
FMO1-AS1	XR_001738291.3	n.599+9847T>C		intron_variant	Intron 3 of 3
FMO1-AS1	XR_922278.4	n.599+9847T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMO6P	ENST00000236166.5	n.1257-2797A>G		intron_variant	Intron 7 of 7	6
FMO6P	ENST00000367754.3	n.1720-2901A>G		intron_variant	Intron 6 of 6	2
FMO6P	ENST00000633725.1	n.25-2807A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32684 AN: 152080 Hom.: 3770 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.215 AC: 32719 AN: 152198 Hom.: 3780 Cov.: 33 AF XY: 0.219 AC XY: 16315 AN XY: 74406

African (AFR) AF: 0.209 AC: 8677 AN: 41532

American (AMR) AF: 0.274 AC: 4186 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2018 AN: 5168

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2372 AN: 10598

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13351 AN: 68002

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.200 Hom.: 11852

Bravo AF: 0.216

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs7885012; hg19: chr1-171127396;