NM_001318857.2:c.152-9951G>T

Variant names:

• chr6-42952811-G-T
• rs9471976
• NM_001318857.2:c.152-9951G>T

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.152-9951G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,944 control chromosomes in the GnomAD database, including 25,099 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 0.56 (25099 hom., cov: 31)
• Consequence: CNPY3-GNMT NM_001318857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 17 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318857.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNPY3-GNMT	NM_001318857.2		c.152-9951G>T		intron	N/A	NP_001305786.1
	CNPY3-GNMT	NM_001318856.2		c.9-9401G>T		intron	N/A	NP_001305785.1
	CNPY3-GNMT	NM_001318858.2		c.152-9951G>T		intron	N/A	NP_001305787.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84990 AN: 151826 Hom.: 25059 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.560 AC: 85084 AN: 151944 Hom.: 25099 Cov.: 31 AF XY: 0.551 AC XY: 40929 AN XY: 74256

African (AFR) AF: 0.736 AC: 30511 AN: 41444

American (AMR) AF: 0.420 AC: 6398 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3472

East Asian (EAS) AF: 0.184 AC: 952 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4814

European-Finnish (FIN) AF: 0.466 AC: 4918 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36403 AN: 67938

Other (OTH) AF: 0.550 AC: 1161 AN: 2112

Alfa AF: 0.536 Hom.: 21648

Bravo AF: 0.563

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.53
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9471976; hg19: chr6-42920549;