rs9471974

Variant names:

• chr6-42951246-T-A
• rs9471974
• NM_001318857.2:c.152-11516T>A

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.152-11516T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,726 control chromosomes in the GnomAD database, including 12,870 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 0.41 (12870 hom., cov: 30)
• Consequence: CNPY3-GNMT NM_001318857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNPY3-GNMT	NM_001318857.2	c.152-11516T>A		intron_variant	Intron 1 of 4		NP_001305786.1
CNPY3-GNMT	NM_001318856.2	c.9-10966T>A		intron_variant	Intron 1 of 5		NP_001305785.1
CNPY3-GNMT	NM_001318858.2	c.152-11516T>A		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: 0.407 AC: 61657 AN: 151612 Hom.: 12865 Cov.: 30

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.407 AC: 61698 AN: 151726 Hom.: 12870 Cov.: 30 AF XY: 0.403 AC XY: 29848 AN XY: 74132

African (AFR) AF: 0.394 AC: 16318 AN: 41382

American (AMR) AF: 0.340 AC: 5189 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1414 AN: 3470

East Asian (EAS) AF: 0.105 AC: 532 AN: 5070

South Asian (SAS) AF: 0.405 AC: 1946 AN: 4804

European-Finnish (FIN) AF: 0.407 AC: 4279 AN: 10524

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30489 AN: 67924

Other (OTH) AF: 0.420 AC: 880 AN: 2094

Alfa AF: 0.430 Hom.: 1792

Bravo AF: 0.399

Asia WGS AF: 0.257 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9471974; hg19: chr6-42918984;