rs1380994

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015668.5(RGS22):​c.340-1320C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,064 control chromosomes in the GnomAD database, including 11,781 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 0.38 ( 11781 hom., cov: 32)

Consequence

RGS22
NM_015668.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.124
Variant links:
Genes affected
RGS22 (HGNC:24499): (regulator of G protein signaling 22) Enables G-protein alpha-subunit binding activity. Predicted to be involved in negative regulation of signal transduction. Located in actin cytoskeleton; cytosol; and fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RGS22NM_015668.5 linkuse as main transcriptc.340-1320C>T intron_variant ENST00000360863.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RGS22ENST00000360863.11 linkuse as main transcriptc.340-1320C>T intron_variant 1 NM_015668.5 P3Q8NE09-1

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
58470
AN:
151946
Hom.:
11770
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.274
Gnomad AMI
AF:
0.413
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.347
Gnomad EAS
AF:
0.552
Gnomad SAS
AF:
0.370
Gnomad FIN
AF:
0.469
Gnomad MID
AF:
0.334
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.371
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.385
AC:
58506
AN:
152064
Hom.:
11781
Cov.:
32
AF XY:
0.390
AC XY:
29009
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.484
Gnomad4 ASJ
AF:
0.347
Gnomad4 EAS
AF:
0.552
Gnomad4 SAS
AF:
0.370
Gnomad4 FIN
AF:
0.469
Gnomad4 NFE
AF:
0.408
Gnomad4 OTH
AF:
0.369
Alfa
AF:
0.403
Hom.:
26064
Bravo
AF:
0.383
Asia WGS
AF:
0.485
AC:
1687
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.0
DANN
Benign
0.34

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1380994; hg19: chr8-101085778; API