rs2179652

Variant names:

• chr1-192800696-C-T
• rs2179652
• ENST00000429211.2:n.126C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429211.2(ENSG00000226814):​n.126C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 206,522 control chromosomes in the GnomAD database, including 32,369 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 0.56 (23688 hom., cov: 30)
  • Exomes 𝑓: 0.57 (8681 hom.)
• Consequence: ENSG00000226814 ENST00000429211.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• Publications: 8 publications found

Genes affected

ENSG00000226814 (HGNC:):

RGS2-AS1 (HGNC:49018): (RSG2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429211.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226814	ENST00000429211.2	TSL:6	n.126C>T		non_coding_transcript_exon	Exon 1 of 1
	RGS2-AS1	ENST00000644058.2		n.202-34502G>A		intron	N/A
	RGS2-AS1	ENST00000644134.1		n.105-34502G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84303 AN: 151642 Hom.: 23662 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.568 AC: 31098 AN: 54762 Hom.: 8681 Cov.: 0 AF XY: 0.571 AC XY: 18458 AN XY: 32344

African (AFR) AF: 0.644 AC: 1084 AN: 1682

American (AMR) AF: 0.506 AC: 3378 AN: 6676

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 476 AN: 748

East Asian (EAS) AF: 0.657 AC: 2356 AN: 3586

South Asian (SAS) AF: 0.627 AC: 4009 AN: 6398

European-Finnish (FIN) AF: 0.478 AC: 2626 AN: 5496

Middle Eastern (MID) AF: 0.655 AC: 1051 AN: 1604

European-Non Finnish (NFE) AF: 0.565 AC: 14952 AN: 26442

Other (OTH) AF: 0.547 AC: 1166 AN: 2130

GnomAD4 genome AF: 0.556 AC: 84375 AN: 151760 Hom.: 23688 Cov.: 30 AF XY: 0.553 AC XY: 40979 AN XY: 74132

African (AFR) AF: 0.620 AC: 25649 AN: 41386

American (AMR) AF: 0.528 AC: 8051 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3258 AN: 5170

South Asian (SAS) AF: 0.606 AC: 2910 AN: 4802

European-Finnish (FIN) AF: 0.413 AC: 4337 AN: 10494

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36107 AN: 67900

Other (OTH) AF: 0.554 AC: 1163 AN: 2098

Alfa AF: 0.549 Hom.: 3443

Bravo AF: 0.563

Asia WGS AF: 0.644 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2179652; hg19: chr1-192769826;