rs1736565

Positions:

• chr1-171143351-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 4P and 8B. PP3_Strong BA1

The ENST00000236166.4(FMO6P):​n.313C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 453,950 control chromosomes in the GnomAD database, including 78,501 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (28735 hom., cov: 32)
  • Exomes 𝑓: 0.57 (49766 hom.)
• Consequence: FMO6P ENST00000236166.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763

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 Likely_benign. Variant got -4 ACMG points.

• PP3: BayesDel_noAF computational evidence supports a deleterious effect, 0.65
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMO6P	NR_002601.1	n.906-3127C>T		intron_variant, non_coding_transcript_variant
LOC105371611	XR_922278.4	n.600-21488G>A		intron_variant, non_coding_transcript_variant
LOC105371611	XR_001738291.3	n.600-21488G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMO6P	ENST00000236166.4	n.313C>T		non_coding_transcript_exon_variant	2/8
FMO6P	ENST00000367754.3	n.906-3127C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000669750.1	n.533+24753G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92034 AN: 151914 Hom.: 28677 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.562

GnomAD3 exomes AF: 0.584 AC: 77774 AN: 133268 Hom.: 23126 AF XY: 0.578 AC XY: 41921 AN XY: 72538

Gnomad AFR exome AF: 0.771

Gnomad AMR exome AF: 0.677

Gnomad ASJ exome AF: 0.507

Gnomad EAS exome AF: 0.595

Gnomad SAS exome AF: 0.609

Gnomad FIN exome AF: 0.535

Gnomad NFE exome AF: 0.528

Gnomad OTH exome AF: 0.524

GnomAD4 exome AF: 0.569 AC: 171829 AN: 301918 Hom.: 49766 Cov.: 0 AF XY: 0.569 AC XY: 97922 AN XY: 171966

Gnomad4 AFR exome AF: 0.765

Gnomad4 AMR exome AF: 0.677

Gnomad4 ASJ exome AF: 0.504

Gnomad4 EAS exome AF: 0.589

Gnomad4 SAS exome AF: 0.610

Gnomad4 FIN exome AF: 0.542

Gnomad4 NFE exome AF: 0.533

Gnomad4 OTH exome AF: 0.549

GnomAD4 genome AF: 0.606 AC: 92151 AN: 152032 Hom.: 28735 Cov.: 32 AF XY: 0.606 AC XY: 45012 AN XY: 74292

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.562

Alfa AF: 0.540 Hom.: 31091

Bravo AF: 0.617

Asia WGS AF: 0.596 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Pathogenic	0.65
CADD	Benign	8.4
DANN	Uncertain	1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736565; hg19: chr1-171112490;