ENST00000687018.1:n.*2161C>T

Variant names:

• chr1-240775321-G-A
• rs6700378
• ENST00000687018.1:n.*2161C>T

Variant summary

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

The ENST00000687018.1(RGS7):​n.*2161C>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 0.172 in 152,120 control chromosomes in the GnomAD database, including 3,033 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 0.17 (3033 hom., cov: 33)
• Consequence: RGS7 ENST00000687018.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 1 publications found

Genes affected

RGS7 (HGNC:10003): (regulator of G protein signaling 7) Enables G-protein beta-subunit binding activity and GTPase activator activity. Involved in positive regulation of GTPase activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

RGS7 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: G2P

ENSG00000226919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687018.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS7	NM_001374806.1		c.*899C>T		3_prime_UTR	Exon 17 of 17	NP_001361735.1
	RGS7	NM_001374807.1		c.*842C>T		3_prime_UTR	Exon 16 of 16	NP_001361736.1
	RGS7	NM_001374808.1		c.*899C>T		3_prime_UTR	Exon 19 of 19	NP_001361737.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS7	ENST00000687018.1		n.*2161C>T		non_coding_transcript_exon	Exon 18 of 18	ENSP00000509943.1
	RGS7	ENST00000687018.1		n.*2161C>T		3_prime_UTR	Exon 18 of 18	ENSP00000509943.1
	RGS7	ENST00000690539.1		c.1360-7043C>T		intron	N/A	ENSP00000510322.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26150 AN: 152002 Hom.: 3022 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.172 AC: 26196 AN: 152120 Hom.: 3033 Cov.: 33 AF XY: 0.167 AC XY: 12451 AN XY: 74372

African (AFR) AF: 0.330 AC: 13709 AN: 41482

American (AMR) AF: 0.0976 AC: 1491 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3472

East Asian (EAS) AF: 0.130 AC: 670 AN: 5158

South Asian (SAS) AF: 0.102 AC: 491 AN: 4814

European-Finnish (FIN) AF: 0.0771 AC: 817 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8163 AN: 68006

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.141 Hom.: 380

Bravo AF: 0.180

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
DANN	Benign	0.40
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6700378; hg19: chr1-240938621;