rs4820237

Variant names:

• chr22-36498606-C-A
• rs4820237
• NM_001102371.2:c.1217-450G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-36498606-C-A
• chr22-36498606-C-G
• chr22-36498606-C-T

Variant summary

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

The NM_001102371.2(FOXRED2):​c.1217-450G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,062 control chromosomes in the GnomAD database, including 25,533 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 0.54 (25533 hom., cov: 32)
• Consequence: FOXRED2 NM_001102371.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 7 publications found

Genes affected

FOXRED2 (HGNC:26264): (FAD dependent oxidoreductase domain containing 2) Enables flavin adenine dinucleotide binding activity. Involved in ubiquitin-dependent ERAD pathway. Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102371.2. 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
	FOXRED2	NM_001102371.2	MANE Select	c.1217-450G>T		intron	N/A	NP_001095841.1
	FOXRED2	NM_001438722.1		c.1217-450G>T		intron	N/A	NP_001425651.1
	FOXRED2	NM_024955.6		c.1217-450G>T		intron	N/A	NP_079231.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXRED2	ENST00000397224.9	TSL:1 MANE Select	c.1217-450G>T		intron	N/A	ENSP00000380401.4
	FOXRED2	ENST00000216187.10	TSL:1	c.1217-450G>T		intron	N/A	ENSP00000216187.6
	FOXRED2	ENST00000397223.4	TSL:1	c.1217-450G>T		intron	N/A	ENSP00000380400.4

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82323 AN: 151944 Hom.: 25530 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.542 AC: 82345 AN: 152062 Hom.: 25533 Cov.: 32 AF XY: 0.535 AC XY: 39785 AN XY: 74310

African (AFR) AF: 0.255 AC: 10590 AN: 41488

American (AMR) AF: 0.662 AC: 10100 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1993 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1238 AN: 5166

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4828

European-Finnish (FIN) AF: 0.617 AC: 6512 AN: 10552

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48128 AN: 67980

Other (OTH) AF: 0.587 AC: 1234 AN: 2104

Alfa AF: 0.655 Hom.: 54183

Bravo AF: 0.536

Asia WGS AF: 0.309 AC: 1075 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	0.26
DANN	Benign	0.55
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4820237; hg19: chr22-36894653;