rs72734930

Variant names:

• chr1-192543429-G-A
• rs72734930
• ENST00000434300.3:n.234+23718C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-192543429-G-A
• chr1-192543429-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000642855.1(RGS2-AS1):​n.409+23718C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 152,172 control chromosomes in the GnomAD database, including 50 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 0.019 (50 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 6 publications found

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0188 (2864/152172) while in subpopulation AMR AF = 0.0272 (415/15284). AF 95% confidence interval is 0.025. There are 50 homozygotes in GnomAd4. There are 1338 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 50 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642855.1. 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
	RGS2-AS1	ENST00000434300.3	TSL:5	n.234+23718C>T		intron	N/A
	RGS2-AS1	ENST00000642855.1		n.409+23718C>T		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.634+23718C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2866 AN: 152056 Hom.: 50 Cov.: 32

Gnomad AFR AF: 0.00432

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0178

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0188 AC: 2864 AN: 152172 Hom.: 50 Cov.: 32 AF XY: 0.0180 AC XY: 1338 AN XY: 74392

African (AFR) AF: 0.00431 AC: 179 AN: 41512

American (AMR) AF: 0.0272 AC: 415 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0586 AC: 203 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4826

European-Finnish (FIN) AF: 0.0113 AC: 119 AN: 10574

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1689 AN: 68010

Other (OTH) AF: 0.0176 AC: 37 AN: 2106

Alfa AF: 0.00987 Hom.: 2

Bravo AF: 0.0194

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.75
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs72734930; hg19: chr1-192512559;