12-56305839-A-G

Variant names:

• chr12-56305839-A-G
• rs10876882
• ENST00000549318.5:c.569+4127T>C

Variant summary

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

The ENST00000549318.5(ENSG00000144785):​c.569+4127T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 144,540 control chromosomes in the GnomAD database, including 49,632 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 0.80 (49632 hom., cov: 23)
• Consequence: ENSG00000144785 ENST00000549318.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 17 publications found

Genes affected

ENSG00000144785 (HGNC:):

CNPY2-AS1 (HGNC:55480): (CNPY2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549318.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000144785	ENST00000549318.5	TSL:5	c.569+4127T>C		intron	N/A	ENSP00000446743.1	F8W031
	ENSG00000144785	ENST00000547423.5	TSL:4	c.204+9012T>C		intron	N/A	ENSP00000446506.1	F8VP03
	ENSG00000144785	ENST00000548360.1	TSL:4	c.205-5619T>C		intron	N/A	ENSP00000447042.1	F8W1U5

Frequencies

GnomAD3 genomes AF: 0.801 AC: 115717 AN: 144440 Hom.: 49641 Cov.: 23

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.947

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.801 AC: 115724 AN: 144540 Hom.: 49632 Cov.: 23 AF XY: 0.804 AC XY: 55692 AN XY: 69268

African (AFR) AF: 0.461 AC: 18053 AN: 39202

American (AMR) AF: 0.879 AC: 12163 AN: 13836

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3299 AN: 3446

East Asian (EAS) AF: 0.965 AC: 4830 AN: 5004

South Asian (SAS) AF: 0.979 AC: 4637 AN: 4736

European-Finnish (FIN) AF: 0.941 AC: 7369 AN: 7828

Middle Eastern (MID) AF: 0.943 AC: 264 AN: 280

European-Non Finnish (NFE) AF: 0.929 AC: 62494 AN: 67278

Other (OTH) AF: 0.867 AC: 1756 AN: 2026

Alfa AF: 0.882 Hom.: 108832

Bravo AF: 0.785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10876882;

hg19: chr12-56699623;