rs729800

Positions:

• chr5-134406190-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CDKN2AIPNL	NM_080656.3	c.340-3264T>C		intron_variant		ENST00000458198.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKN2AIPNL	ENST00000458198.3	c.340-3264T>C		intron_variant		1	NM_080656.3	P1

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.583

Alfa AF: 0.674 Hom.: 57389

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs729800; hg19: chr5-133741881;