rs7885012

chr1-171158257-A-G

Variant summary

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

The NR_002601.1(FMO6P):n.1720-2901A>G 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 0.215 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 NR_002601.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FMO6P	NR_002601.1	n.1720-2901A>G		intron_variant, non_coding_transcript_variant
LOC105371611	XR_922278.4	n.599+9847T>C		intron_variant, non_coding_transcript_variant
LOC105371611	XR_001738291.3	n.599+9847T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMO6P	ENST00000236166.4	n.1257-2776A>G		intron_variant, non_coding_transcript_variant
FMO6P	ENST00000367754.3	n.1720-2901A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000669750.1	n.533+9847T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.183

Alfa AF: 0.193 Hom.: 4758

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7885012; hg19: chr1-171127396;