rs1894560

Variant names:

• chr6-36737010-G-A
• rs1894560
• ENST00000494644.1:n.-40G>A

Variant summary

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

The ENST00000494644.1(GPR166P):​n.-40G>A variant causes a upstream gene change. The variant allele was found at a frequency of 0.314 in 152,084 control chromosomes in the GnomAD database, including 7,700 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 0.31 (7698 hom., cov: 32)
  • Exomes 𝑓: 0.35 (2 hom.)
• Consequence: GPR166P ENST00000494644.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.86
• Publications: 6 publications found

Genes affected

GPR166P (HGNC:23626):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR166P	ENST00000494644.1	n.-40G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47737 AN: 151904 Hom.: 7695 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.355 AC: 22 AN: 62 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 16 AN XY: 32

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.405 AC: 17 AN: 42

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.314 AC: 47773 AN: 152022 Hom.: 7698 Cov.: 32 AF XY: 0.306 AC XY: 22741 AN XY: 74320

African (AFR) AF: 0.300 AC: 12435 AN: 41432

American (AMR) AF: 0.234 AC: 3580 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5168

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4822

European-Finnish (FIN) AF: 0.269 AC: 2847 AN: 10580

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24557 AN: 67958

Other (OTH) AF: 0.293 AC: 618 AN: 2110

Alfa AF: 0.342 Hom.: 14752

Bravo AF: 0.310

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs1894560; hg19: chr6-36704787;