Genetic Variant RGS2-AS1:n.165-467G>A (chr1-192567683-C-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The XR_002958418.2(LOC105371664):n.288-467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: XR_002958418.2 is not a MANE Select or MANE Plus Clinical transcript for LOC105371664; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

LOC105371664
XR_002958418.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.127

Publications

0 publications found

Variant links:

Genes affected

RGS2-AS1 (HGNC:49018): ()

RGS2-AS1 links:

LOC105371664 (HGNC:):

LOC105371664 links:

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new If you want to explore the variant's impact on the transcript XR_002958418.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000434300.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
RGS2-AS1 ENST00000434300.3	TSL:5	n.165-467G>A	intron	Intron 2 of 3	Prot:
RGS2-AS1 ENST00000642855.1		n.340-467G>A	intron	Intron 3 of 7	Prot:
RGS2-AS1 ENST00000644058.2		n.565-467G>A	intron	Intron 4 of 5	Prot:

RGS2-AS1 ENST00000434300.3

TSL:5

HGVSc / HGVSpn.165-467G>A

Exon rankIntron 2 of 3

intron

Prot:

RGS2-AS1 ENST00000642855.1

HGVSc / HGVSpn.340-467G>A

Exon rankIntron 3 of 7

intron

Prot:

RGS2-AS1 ENST00000644058.2

HGVSc / HGVSpn.565-467G>A

Exon rankIntron 4 of 5

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	2.8
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.2
DANN	Benign	0.73
GPN-Star LLR	N/A	0.28
GPN-Star score	N/A	-0.28
PhyloP100	Benign	0.13

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence