ENST00000415437.1:n.1754C>T

Variant names:

• chr1-163212144-C-T
• rs2036702
• ENST00000415437.1:n.1754C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000415437.1(RGS5-AS1):​n.1754C>T variant causes a non coding transcript exon 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: 32)
• Consequence: RGS5-AS1 ENST00000415437.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 5 publications found

Genes affected

RGS5-AS1 (HGNC:40504): (RGS5 antisense RNA 1)

RGS5 (HGNC:10001): (regulator of G protein signaling 5) This locus represents naturally occurring readthrough transcription between the neighboring LOC127814295 (uncharacterized LOC127814295) and RGS5 (regulator of G-protein signaling 5) genes on chromosome 1. Some variants of the readthrough transcript encode novel proteins with unique N-termini. [provided by RefSeq, Nov 2022]

RGS5 Gene-Disease associations (from GenCC):

• essential hypertension, genetic

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS5-AS1	NR_110699.1	n.1754C>T		non_coding_transcript_exon_variant	Exon 4 of 4
RGS5	NM_001414472.1	c.65+36386G>A		intron_variant	Intron 3 of 6		NP_001401401.1
RGS5	NM_001414473.1	c.65+36386G>A		intron_variant	Intron 5 of 8		NP_001401402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS5-AS1	ENST00000415437.1	n.1754C>T		non_coding_transcript_exon_variant	Exon 4 of 4	2
RGS5	ENST00000367903.7	c.69+5382G>A		intron_variant	Intron 1 of 5	3		ENSP00000356879.3
RGS5	ENST00000618415.4	c.-280-43776G>A		intron_variant	Intron 2 of 5	4		ENSP00000480891.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.78
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2036702; hg19: chr1-163181934;