chr7-1088069-G-T

Position:

• chr7-1088069-G-T

Variant summary

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

The NM_001318252.2(C7orf50):​c.129+39188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 152,268 control chromosomes in the GnomAD database, including 66 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 0.017 (66 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: C7orf50 NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

C7orf50 (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

GPER1 (HGNC:4485): (G protein-coupled estrogen receptor 1) This gene encodes a multi-pass membrane protein that localizes to the endoplasmic reticulum and a member of the G-protein coupled receptor 1 family. This receptor binds estrogen and activates multiple downstream signaling pathways, leading to stimulation of adenylate cyclase and an increase in cyclic AMP levels, while also promoting intracellular calcium mobilization and synthesis of phosphatidylinositol 3,4,5-trisphosphate in the nucleus. This protein therefore plays a role in the rapid nongenomic signaling events widely observed following stimulation of cells and tissues with estrogen. This receptor has been shown to play a role in diverse biological processes, including bone and nervous system development, metabolism, cognition, male fertility and uterine function. [provided by RefSeq, Aug 2017]

C7orf50 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C7orf50	NM_001318252.2	c.129+39188C>A		intron_variant		ENST00000397098.8	NP_001305181.1
GPER1	NM_001098201.3	c.-575G>T		upstream_gene_variant		ENST00000397088.4	NP_001091671.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C7orf50	ENST00000397098.8	c.129+39188C>A		intron_variant		1	NM_001318252.2	ENSP00000380286.3
GPER1	ENST00000397088.4	c.-575G>T		upstream_gene_variant		1	NM_001098201.3	ENSP00000380277.3

Frequencies

GnomAD3 genomes AF: 0.0168 AC: 2557 AN: 152150 Hom.: 66 Cov.: 33

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00694

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0153

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 84 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 62

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0168 AC: 2553 AN: 152268 Hom.: 66 Cov.: 33 AF XY: 0.0186 AC XY: 1387 AN XY: 74452

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.00693

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.00504 Hom.: 2

Bravo AF: 0.0154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.35

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: rs33987461; hg19: chr7-1127705;