rs9462856

Positions:

• chr6-42958286-T-C

Variant summary

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

The NR_134890.2(CNPY3-GNMT):​n.340-4476T>C variant causes a intron, non coding transcript 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 NR_134890.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

CNPY3-GNMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CNPY3-GNMT	NR_134890.2	n.340-4476T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.569

Alfa AF: 0.546 Hom.: 13334

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9462856; hg19: chr6-42926024;