rs1795244

Variant names:

• chr1-171149882-T-C
• rs1795244
• ENST00000236166.5:n.827+123T>C

Variant summary

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

The ENST00000236166.5(FMO6P):​n.827+123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 369,326 control chromosomes in the GnomAD database, including 61,047 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 0.60 (28422 hom., cov: 32)
  • Exomes 𝑓: 0.54 (32625 hom.)
• Consequence: FMO6P ENST00000236166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000236166.5. 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
	FMO6P	NR_002601.1		n.1290+123T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMO6P	ENST00000236166.5	TSL:6	n.827+123T>C		intron	N/A
	FMO6P	ENST00000367754.3	TSL:2	n.1290+123T>C		intron	N/A
	FMO6P	ENST00000639957.1	TSL:5	n.757+123T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90568 AN: 151924 Hom.: 28357 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.542 AC: 117846 AN: 217284 Hom.: 32625 AF XY: 0.548 AC XY: 65785 AN XY: 120024

African (AFR) AF: 0.799 AC: 4428 AN: 5542

American (AMR) AF: 0.645 AC: 8614 AN: 13348

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 2316 AN: 4958

East Asian (EAS) AF: 0.641 AC: 5489 AN: 8560

South Asian (SAS) AF: 0.604 AC: 25589 AN: 42368

European-Finnish (FIN) AF: 0.499 AC: 7310 AN: 14642

Middle Eastern (MID) AF: 0.476 AC: 339 AN: 712

European-Non Finnish (NFE) AF: 0.499 AC: 58398 AN: 116972

Other (OTH) AF: 0.527 AC: 5363 AN: 10182

GnomAD4 genome AF: 0.596 AC: 90687 AN: 152042 Hom.: 28422 Cov.: 32 AF XY: 0.596 AC XY: 44330 AN XY: 74320

African (AFR) AF: 0.798 AC: 33107 AN: 41482

American (AMR) AF: 0.600 AC: 9159 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3298 AN: 5172

South Asian (SAS) AF: 0.621 AC: 2995 AN: 4822

European-Finnish (FIN) AF: 0.480 AC: 5064 AN: 10550

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33805 AN: 67972

Other (OTH) AF: 0.544 AC: 1149 AN: 2112

Alfa AF: 0.537 Hom.: 63350

Bravo AF: 0.611

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.43
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1795244; hg19: chr1-171119021;