15-55657884-C-A

Variant names:

• chr15-55657884-C-A
• rs11071200
• NM_173814.6:c.2041+14561G>T

Variant summary

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

The NM_173814.6(PRTG):​c.2041+14561G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,942 control chromosomes in the GnomAD database, including 3,921 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 0.22 (3921 hom., cov: 33)
• Consequence: PRTG NM_173814.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 8 publications found

Genes affected

PRTG (HGNC:26373): (protogenin) This gene encodes a member of the immunoglobulin superfamily. The encoded transmembrane protein has been associated with the development of various tissues, especially neurogenesis. It has been suggested that this gene may be associated with attention deficit hyperactivity disorder (ADHD). [provided by RefSeq, Nov 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRTG	NM_173814.6	c.2041+14561G>T		intron_variant	Intron 11 of 19	ENST00000389286.9	NP_776175.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRTG	ENST00000389286.9	c.2041+14561G>T		intron_variant	Intron 11 of 19	1	NM_173814.6	ENSP00000373937.4
PRTG	ENST00000561465.1	c.647-1530G>T		intron_variant	Intron 3 of 3	2		ENSP00000453160.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33287 AN: 151824 Hom.: 3908 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.220 AC: 33353 AN: 151942 Hom.: 3921 Cov.: 33 AF XY: 0.217 AC XY: 16088 AN XY: 74258

African (AFR) AF: 0.280 AC: 11596 AN: 41440

American (AMR) AF: 0.165 AC: 2514 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3468

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5182

South Asian (SAS) AF: 0.0877 AC: 422 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2549 AN: 10550

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14930 AN: 67924

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.211 Hom.: 4681

Bravo AF: 0.216

Asia WGS AF: 0.105 AC: 365 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		0.24
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: rs11071200; hg19: chr15-55950082;