chr22-36495811-C-A

Position:

• chr22-36495811-C-A

Variant summary

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

The NM_001102371.2(FOXRED2):​c.1624+156G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,190 control chromosomes in the GnomAD database, including 14,541 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 0.39 (14541 hom., cov: 33)
• Consequence: FOXRED2 NM_001102371.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXRED2	NM_001102371.2	c.1624+156G>T		intron_variant		ENST00000397224.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXRED2	ENST00000397224.9	c.1624+156G>T		intron_variant		1	NM_001102371.2	P1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58821 AN: 152072 Hom.: 14539 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.387 AC: 58823 AN: 152190 Hom.: 14541 Cov.: 33 AF XY: 0.379 AC XY: 28192 AN XY: 74406

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.0862

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.437

Alfa AF: 0.512 Hom.: 27140

Bravo AF: 0.393

Asia WGS AF: 0.160 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.5
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756219; hg19: chr22-36891858; COSMIC: COSV53400241;