NM_080656.3:c.340-3264T>C

Variant names:

• chr5-134406190-A-G
• rs729800
• NM_080656.3:c.340-3264T>C

Variant summary

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

The NM_080656.3(CDKN2AIPNL):​c.340-3264T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,122 control chromosomes in the GnomAD database, including 26,599 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 0.57 (26599 hom., cov: 33)
• Consequence: CDKN2AIPNL NM_080656.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 7 publications found

Genes affected

CDKN2AIPNL (HGNC:30545): (CDKN2A interacting protein N-terminal like) Predicted to be active in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKN2AIPNL	NM_080656.3	c.340-3264T>C		intron_variant	Intron 2 of 2	ENST00000458198.3	NP_542387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKN2AIPNL	ENST00000458198.3	c.340-3264T>C		intron_variant	Intron 2 of 2	1	NM_080656.3	ENSP00000394183.2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86493 AN: 152004 Hom.: 26604 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.569 AC: 86489 AN: 152122 Hom.: 26599 Cov.: 33 AF XY: 0.563 AC XY: 41867 AN XY: 74366

African (AFR) AF: 0.339 AC: 14088 AN: 41498

American (AMR) AF: 0.497 AC: 7588 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2599 AN: 5168

South Asian (SAS) AF: 0.559 AC: 2695 AN: 4824

European-Finnish (FIN) AF: 0.674 AC: 7133 AN: 10578

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.708 AC: 48140 AN: 67988

Other (OTH) AF: 0.583 AC: 1232 AN: 2114

Alfa AF: 0.647 Hom.: 90290

Bravo AF: 0.542

Asia WGS AF: 0.535 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs729800; hg19: chr5-133741881;