1-240775321-G-C

Variant names:

• chr1-240775321-G-C
• rs6700378
• NM_001374806.1:c.*899C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001374806.1(RGS7):​c.*899C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: RGS7 NM_001374806.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001374806.1. 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
	RGS7	NM_001374806.1		c.*899C>G		3_prime_UTR	Exon 17 of 17	NP_001361735.1
	RGS7	NM_001374807.1		c.*842C>G		3_prime_UTR	Exon 16 of 16	NP_001361736.1	A0A8I5KZ50
	RGS7	NM_001374808.1		c.*899C>G		3_prime_UTR	Exon 19 of 19	NP_001361737.1	B7Z257

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS7	ENST00000690539.1		c.1360-7043C>G		intron	N/A	ENSP00000510322.1	A0A8I5KRS1
	RGS7	ENST00000687018.1		n.*2161C>G		non_coding_transcript_exon	Exon 18 of 18	ENSP00000509943.1	A0A8I5QKX5
	RGS7	ENST00000687018.1		n.*2161C>G		3_prime_UTR	Exon 18 of 18	ENSP00000509943.1	A0A8I5QKX5

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.015
DANN	Benign	0.34
PhyloP100		-2.4

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; COSMIC: COSV58529549;