rs11752813

Positions:

• chr6-42960279-C-G

Variant summary

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

The NR_134890.2(CNPY3-GNMT):​n.340-2483C>G 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 0.403 in 152,226 control chromosomes in the GnomAD database, including 12,748 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 0.40 (12748 hom., cov: 34)
• Consequence: CNPY3-GNMT NR_134890.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

CNPY3-GNMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNPY3-GNMT	NR_134890.2	n.340-2483C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61291 AN: 152108 Hom.: 12744 Cov.: 34

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.403 AC: 61328 AN: 152226 Hom.: 12748 Cov.: 34 AF XY: 0.399 AC XY: 29685 AN XY: 74444

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.414

Alfa AF: 0.431 Hom.: 1921

Bravo AF: 0.394

Asia WGS AF: 0.257 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752813; hg19: chr6-42928017;