chr20-25619019-A-G

Variant names:

• chr20-25619019-A-G
• rs8120594
• NM_152667.3:c.91-2438T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152667.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NANP	NM_152667.3	MANE Select	c.91-2438T>C		intron	N/A	NP_689880.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NANP	ENST00000304788.4	TSL:1 MANE Select	c.91-2438T>C		intron	N/A	ENSP00000302441.3

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

African (AFR) AF: 0.455 AC: 18811 AN: 41386

American (AMR) AF: 0.0876 AC: 1340 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3466

East Asian (EAS) AF: 0.0676 AC: 348 AN: 5150

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4816

European-Finnish (FIN) AF: 0.0593 AC: 629 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2890 AN: 68024

Other (OTH) AF: 0.138 AC: 291 AN: 2110

Alfa AF: 0.122 Hom.: 513

Bravo AF: 0.180

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.0060
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: rs8120594; hg19: chr20-25599655;