2-219184665-A-G

Position:

• chr2-219184665-A-G

Variant summary

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

The NM_024293.6(RETREG2):​c.*2036A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,180 control chromosomes in the GnomAD database, including 68,948 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 0.95 (68947 hom., cov: 30)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: RETREG2 NM_024293.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

RETREG2 (HGNC:28450): (reticulophagy regulator family member 2) Predicted to be integral component of membrane. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RETREG2	NM_024293.6	c.*2036A>G		3_prime_UTR_variant	9/9	ENST00000430297.7
RETREG2	NM_001321109.2	c.*2036A>G		3_prime_UTR_variant	9/9
RETREG2	NM_001321110.2	c.*2036A>G		3_prime_UTR_variant	9/9
RETREG2	XM_005246848.4	c.*2036A>G		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RETREG2	ENST00000430297.7	c.*2036A>G		3_prime_UTR_variant	9/9	1	NM_024293.6	P1

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144399 AN: 152062 Hom.: 68906 Cov.: 30

Gnomad AFR AF: 0.841

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.941

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.961

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.950 AC: 144499 AN: 152178 Hom.: 68947 Cov.: 30 AF XY: 0.950 AC XY: 70670 AN XY: 74404

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.961

Alfa AF: 0.970 Hom.: 8907

Bravo AF: 0.944

Asia WGS AF: 0.957 AC: 3330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.46

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: rs2385393; hg19: chr2-220049387;