rs958075

Variant names:

• chr20-25614487-G-A
• rs958075
• NM_152667.3:c.*1438C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-25614487-G-A
• chr20-25614487-G-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.*1438C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,756 control chromosomes in the GnomAD database, including 10,888 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 0.36 (10888 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NANP NM_152667.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NANP	NM_152667.3	c.*1438C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000304788.4	NP_689880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NANP	ENST00000304788.4	c.*1438C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_152667.3	ENSP00000302441.3

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54948 AN: 151640 Hom.: 10882 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.400

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.362 AC: 54967 AN: 151756 Hom.: 10888 Cov.: 32 AF XY: 0.362 AC XY: 26803 AN XY: 74142

African (AFR) AF: 0.241 AC: 9966 AN: 41366

American (AMR) AF: 0.464 AC: 7071 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3470

East Asian (EAS) AF: 0.0157 AC: 81 AN: 5168

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4806

European-Finnish (FIN) AF: 0.386 AC: 4042 AN: 10472

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28402 AN: 67922

Other (OTH) AF: 0.399 AC: 841 AN: 2110

Alfa AF: 0.398 Hom.: 3722

Bravo AF: 0.361

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.012
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: rs958075; hg19: chr20-25595123;