rs8140217

Variant names:

• chr22-38821996-G-A
• rs8140217
• NM_014293.4:c.*613C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-38821996-G-A
• chr22-38821996-G-C
• chr22-38821996-G-T

Variant summary

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

The NM_014293.4(NPTXR):​c.*613C>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 0.172 in 146,452 control chromosomes in the GnomAD database, including 2,181 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 0.17 (2141 hom., cov: 29)
  • Exomes 𝑓: 0.11 (40 hom.)
• Consequence: NPTXR NM_014293.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 7 publications found

Genes affected

NPTXR (HGNC:7954): (neuronal pentraxin receptor) This gene encodes a protein similar to the rat neuronal pentraxin receptor. The rat pentraxin receptor is an integral membrane protein that is thought to mediate neuronal uptake of the snake venom toxin, taipoxin, and its transport into the synapses. Studies in rat indicate that translation of this mRNA initiates at a non-AUG (CUG) codon. This may also be true for mouse and human, based on strong sequence conservation amongst these species. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014293.4. 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
	NPTXR	NM_014293.4	MANE Select	c.*613C>T		3_prime_UTR	Exon 5 of 5	NP_055108.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPTXR	ENST00000333039.4	TSL:1 MANE Select	c.*613C>T		3_prime_UTR	Exon 5 of 5	ENSP00000327545.3
	NPTXR	ENST00000718437.1		c.*613C>T		3_prime_UTR	Exon 5 of 5	ENSP00000520822.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 24641 AN: 141870 Hom.: 2138 Cov.: 29

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.112 AC: 498 AN: 4454 Hom.: 40 Cov.: 0 AF XY: 0.110 AC XY: 265 AN XY: 2408

African (AFR) AF: 0.0238 AC: 1 AN: 42

American (AMR) AF: 0.0689 AC: 69 AN: 1002

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 1 AN: 16

East Asian (EAS) AF: 0.00 AC: 0 AN: 112

South Asian (SAS) AF: 0.0878 AC: 26 AN: 296

European-Finnish (FIN) AF: 0.159 AC: 77 AN: 484

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.131 AC: 304 AN: 2318

Other (OTH) AF: 0.100 AC: 18 AN: 180

GnomAD4 genome AF: 0.174 AC: 24658 AN: 141998 Hom.: 2141 Cov.: 29 AF XY: 0.177 AC XY: 12096 AN XY: 68258

African (AFR) AF: 0.163 AC: 6290 AN: 38558

American (AMR) AF: 0.154 AC: 2013 AN: 13040

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 710 AN: 3422

East Asian (EAS) AF: 0.0272 AC: 118 AN: 4332

South Asian (SAS) AF: 0.163 AC: 710 AN: 4366

European-Finnish (FIN) AF: 0.251 AC: 2192 AN: 8730

Middle Eastern (MID) AF: 0.236 AC: 59 AN: 250

European-Non Finnish (NFE) AF: 0.179 AC: 11869 AN: 66430

Other (OTH) AF: 0.189 AC: 373 AN: 1970

Alfa AF: 0.165 Hom.: 5660

Bravo AF: 0.157

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.56

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: rs8140217; hg19: chr22-39218001;