rs1861960

Positions:

• chr7-155492440-T-G

Variant summary

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

The ENST00000406197.5(CNPY1):​c.*47+10581A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,190 control chromosomes in the GnomAD database, including 43,038 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 0.75 (43038 hom., cov: 34)
• Consequence: CNPY1 ENST00000406197.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

CNPY1 (HGNC:27786): (canopy FGF signaling regulator 1) Cnpy1 is expressed in the midbrain-hindbrain (MHB) boundary in zebrafish, binds FGFR1 (MIM 136350), and plays a role in FGF signaling (Hirate and Okamoto, 2006 [PubMed 16488878]).[supplied by OMIM, Dec 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.155492440T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNPY1	ENST00000406197.5	c.*47+10581A>C		intron_variant		5		ENSP00000384514.1
ENSG00000283128	ENST00000635903.1	n.1217-8555A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113505 AN: 152072 Hom.: 43029 Cov.: 34

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.746 AC: 113555 AN: 152190 Hom.: 43038 Cov.: 34 AF XY: 0.737 AC XY: 54850 AN XY: 74414

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.768

Alfa AF: 0.798 Hom.: 64853

Bravo AF: 0.744

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.3
DANN	Benign	0.78

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: rs1861960; hg19: chr7-155285135; COSMIC: COSV68533814;