rs1861960

Variant names:

• chr7-155492440-T-G
• rs1861960
• ENST00000406197.5:c.*47+10581A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000283128 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNPY1	ENST00000406197.5	c.*47+10581A>C		intron_variant	Intron 4 of 4	5		ENSP00000384514.1
ENSG00000283128	ENST00000635903.1	n.1217-8555A>C		intron_variant	Intron 6 of 8	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

African (AFR) AF: 0.709 AC: 29436 AN: 41502

American (AMR) AF: 0.719 AC: 10997 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1788 AN: 5182

South Asian (SAS) AF: 0.730 AC: 3526 AN: 4828

European-Finnish (FIN) AF: 0.684 AC: 7230 AN: 10574

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54865 AN: 68008

Other (OTH) AF: 0.768 AC: 1626 AN: 2116

Alfa AF: 0.789 Hom.: 88247

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
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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