chr1-109540264-C-T

Variant names:

• chr1-109540264-C-T
• rs7550711
• NM_001393907.1:c.-602+311C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001393907.1(GPR61):​c.-602+311C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 152,210 control chromosomes in the GnomAD database, including 85 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 0.025 (85 hom., cov: 32)
• Consequence: GPR61 NM_001393907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 42 publications found

Genes affected

GPR61 (HGNC:13300): (G protein-coupled receptor 61) This gene belongs to the G-protein coupled receptor 1 family. G protein-coupled receptors contain 7 transmembrane domains and transduce extracellular signals through heterotrimeric G proteins. The protein encoded by this gene is most closely related to biogenic amine receptors. [provided by RefSeq, Jul 2008]

ENSG00000254942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0254 (3868/152210) while in subpopulation NFE AF = 0.0319 (2169/68000). AF 95% confidence interval is 0.0308. There are 85 homozygotes in GnomAd4. There are 1990 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 85 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393907.1. 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
	GPR61	NM_001393907.1	MANE Select	c.-602+311C>T		intron	N/A	NP_001380836.1
	GPR61	NM_031936.6		c.-602+311C>T		intron	N/A	NP_114142.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR61	ENST00000527748.5	TSL:2 MANE Select	c.-602+311C>T		intron	N/A	ENSP00000432456.1
	GPR61	ENST00000689084.1		c.-602+311C>T		intron	N/A	ENSP00000509600.1
	GPR61	ENST00000404129.6	TSL:5	n.-602+311C>T		intron	N/A	ENSP00000385422.2

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3865 AN: 152092 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0173

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

GnomAD4 genome AF: 0.0254 AC: 3868 AN: 152210 Hom.: 85 Cov.: 32 AF XY: 0.0267 AC XY: 1990 AN XY: 74406

African (AFR) AF: 0.0150 AC: 624 AN: 41544

American (AMR) AF: 0.0118 AC: 181 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00436 AC: 21 AN: 4814

European-Finnish (FIN) AF: 0.0643 AC: 682 AN: 10604

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0319 AC: 2169 AN: 68000

Other (OTH) AF: 0.0176 AC: 37 AN: 2108

Alfa AF: 0.0268 Hom.: 138

Bravo AF: 0.0207

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.6
DANN	Benign	0.55
PhyloP100		0.093
PromoterAI		-0.00060	Neutral
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs7550711; hg19: chr1-110082886;