rs2385393

Positions:

• chr2-219184665-A-C
• chr2-219184665-A-G
• chr2-219184665-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024293.6(RETREG2):​c.*2036A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RETREG2	NM_024293.6	c.*2036A>C		3_prime_UTR_variant	9/9	ENST00000430297.7	NP_077269.3
RETREG2	NM_001321109.2	c.*2036A>C		3_prime_UTR_variant	9/9		NP_001308038.1
RETREG2	NM_001321110.2	c.*2036A>C		3_prime_UTR_variant	9/9		NP_001308039.1
RETREG2	XM_005246848.4	c.*2036A>C		3_prime_UTR_variant	10/10		XP_005246905.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RETREG2	ENST00000430297.7	c.*2036A>C		3_prime_UTR_variant	9/9	1	NM_024293.6	ENSP00000395249	P1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.47

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;