7-37743498-C-T

Variant names:

• chr7-37743498-C-T
• rs7780507
• NM_001381946.1:c.*2187C>T

Variant summary

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

The NM_001381946.1(GPR141):​c.*2187C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000726 in 151,504 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000073 (0 hom., cov: 31)
• Consequence: GPR141 NM_001381946.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 4 publications found

Genes affected

GPR141 (HGNC:19997): (G protein-coupled receptor 141) GPR141 is a member of the rhodopsin family of G protein-coupled receptors (GPRs) (Fredriksson et al., 2003 [PubMed 14623098]).[supplied by OMIM, Mar 2008]

ENSG00000290149 (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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR141	NM_001381946.1	c.*2187C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000334425.2	NP_001368875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR141	ENST00000334425.2	c.*2187C>T		3_prime_UTR_variant	Exon 3 of 3	6	NM_001381946.1	ENSP00000334540.1
ENSG00000290149	ENST00000476620.1	c.-110+59595C>T		intron_variant	Intron 1 of 3	4		ENSP00000425858.1
GPR141	ENST00000461610.5	n.232+57915C>T		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0000726 AC: 11 AN: 151504 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000960

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

GnomAD4 genome AF: 0.0000726 AC: 11 AN: 151504 Hom.: 0 Cov.: 31 AF XY: 0.0000947 AC XY: 7 AN XY: 73956

African (AFR) AF: 0.0000242 AC: 1 AN: 41266

American (AMR) AF: 0.0000656 AC: 1 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10328

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 67892

Other (OTH) AF: 0.000960 AC: 2 AN: 2084

Alfa AF: 0.00 Hom.: 2178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.90
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7780507; hg19: chr7-37783100;