chr7-155492440-T-G

Variant names:

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

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]

ENSG00000283128 (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 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

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;