rs9462856

Variant names:

• chr6-42958286-T-C
• rs9462856
• NM_001318857.2:c.152-4476T>C

Variant summary

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

The NM_001318857.2(CNPY3-GNMT):​c.152-4476T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,026 control chromosomes in the GnomAD database, including 28,741 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 0.59 (28741 hom., cov: 32)
• Consequence: CNPY3-GNMT NM_001318857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 31 publications found

Genes affected

CNPY3-GNMT (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNPY3-GNMT	NM_001318857.2	c.152-4476T>C		intron_variant	Intron 1 of 4		NP_001305786.1
CNPY3-GNMT	NM_001318856.2	c.9-3926T>C		intron_variant	Intron 1 of 5		NP_001305785.1
CNPY3-GNMT	NM_001318858.2	c.152-4476T>C		intron_variant	Intron 1 of 4		NP_001305787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89669 AN: 151908 Hom.: 28699 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.590 AC: 89767 AN: 152026 Hom.: 28741 Cov.: 32 AF XY: 0.581 AC XY: 43147 AN XY: 74318

African (AFR) AF: 0.842 AC: 34938 AN: 41486

American (AMR) AF: 0.433 AC: 6605 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3470

East Asian (EAS) AF: 0.184 AC: 952 AN: 5182

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4818

European-Finnish (FIN) AF: 0.465 AC: 4895 AN: 10526

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36434 AN: 67978

Other (OTH) AF: 0.569 AC: 1199 AN: 2106

Alfa AF: 0.546 Hom.: 46640

Bravo AF: 0.599

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.27
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9462856; hg19: chr6-42926024;