rs8120594

chr20-25619019-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152667.3(NANP):c.91-2438T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,054 control chromosomes in the GnomAD database, including 4,540 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 0.16 (4540 hom., cov: 31)
• Consequence: NANP NM_152667.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

NANP (HGNC:16140): (N-acetylneuraminic acid phosphatase) Enables N-acylneuraminate-9-phosphatase activity. Involved in N-acetylneuraminate biosynthetic process. Predicted to be located in cytosol. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NANP	NM_152667.3	c.91-2438T>C		intron_variant		ENST00000304788.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NANP	ENST00000304788.4	c.91-2438T>C		intron_variant		1	NM_152667.3	P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24755 AN: 151936 Hom.: 4515 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0485

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.163 AC: 24834 AN: 152054 Hom.: 4540 Cov.: 31 AF XY: 0.160 AC XY: 11922 AN XY: 74334

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.0876

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.0593

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.138

Alfa AF: 0.113 Hom.: 439

Bravo AF: 0.180

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.6
Dann	Benign	0.60

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: rs8120594; hg19: chr20-25599655;