chr1-171149882-T-C

Position:

• chr1-171149882-T-C

Variant summary

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

The NR_002601.1(FMO6P):​n.1290+123T>C 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 0.565 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 NR_002601.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMO6P	NR_002601.1	n.1290+123T>C		intron_variant, non_coding_transcript_variant
LOC105371611	XR_922278.4	n.599+18222A>G		intron_variant, non_coding_transcript_variant
LOC105371611	XR_001738291.3	n.599+18222A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMO6P	ENST00000236166.4	n.827+123T>C		intron_variant, non_coding_transcript_variant
FMO6P	ENST00000367754.3	n.1290+123T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000669750.1	n.533+18222A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.799

Gnomad4 AMR exome AF: 0.645

Gnomad4 ASJ exome AF: 0.467

Gnomad4 EAS exome AF: 0.641

Gnomad4 SAS exome AF: 0.604

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.499

Gnomad4 OTH exome AF: 0.527

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

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.544

Alfa AF: 0.519 Hom.: 21677

Bravo AF: 0.611

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1795244; hg19: chr1-171119021;