1-182601868-C-T

Position:

• chr1-182601868-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002928.4(RGS16):​c.387+98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,477,400 control chromosomes in the GnomAD database, including 276,972 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 0.55 (24366 hom., cov: 32)
  • Exomes 𝑓: 0.61 (252606 hom.)
• Consequence: RGS16 NM_002928.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

RGS16 (HGNC:9997): (regulator of G protein signaling 16) The protein encoded by this gene belongs to the 'regulator of G protein signaling' family. It inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits. It also may play a role in regulating the kinetics of signaling in the phototransduction cascade. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS16	NM_002928.4	c.387+98G>A		intron_variant		ENST00000367558.6	NP_002919.3
RGS16	XM_024448796.1	c.384+98G>A		intron_variant			XP_024304564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS16	ENST00000367558.6	c.387+98G>A		intron_variant		1	NM_002928.4	ENSP00000356529	P1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83834 AN: 151992 Hom.: 24351 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.588

GnomAD3 exomes AF: 0.637 AC: 154779 AN: 242938 Hom.: 50570 AF XY: 0.637 AC XY: 83999 AN XY: 131864

Gnomad AFR exome AF: 0.353

Gnomad AMR exome AF: 0.795

Gnomad ASJ exome AF: 0.686

Gnomad EAS exome AF: 0.727

Gnomad SAS exome AF: 0.677

Gnomad FIN exome AF: 0.618

Gnomad NFE exome AF: 0.601

Gnomad OTH exome AF: 0.633

GnomAD4 exome AF: 0.614 AC: 813269 AN: 1325290 Hom.: 252606 Cov.: 19 AF XY: 0.616 AC XY: 409944 AN XY: 665398

Gnomad4 AFR exome AF: 0.349

Gnomad4 AMR exome AF: 0.786

Gnomad4 ASJ exome AF: 0.684

Gnomad4 EAS exome AF: 0.710

Gnomad4 SAS exome AF: 0.679

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.602

Gnomad4 OTH exome AF: 0.617

GnomAD4 genome AF: 0.551 AC: 83885 AN: 152110 Hom.: 24366 Cov.: 32 AF XY: 0.557 AC XY: 41414 AN XY: 74344

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.587

Alfa AF: 0.581 Hom.: 4805

Bravo AF: 0.548

Asia WGS AF: 0.648 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs610367; hg19: chr1-182571003;