rs17727535

Positions:

• chr11-35523155-C-T

Variant summary

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

The NM_001001991.3(PAMR1):​c.73+2358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,068 control chromosomes in the GnomAD database, including 3,505 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 0.21 (3505 hom., cov: 32)
• Consequence: PAMR1 NM_001001991.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

Genes affected

PAMR1 (HGNC:24554): (peptidase domain containing associated with muscle regeneration 1) Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAMR1	NM_001001991.3	c.73+2358G>A		intron_variant		ENST00000619888.5
PAMR1	NM_001282675.2	c.-155+5797G>A		intron_variant
PAMR1	NM_001282676.2	c.73+2358G>A		intron_variant
PAMR1	NM_015430.4	c.73+2358G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAMR1	ENST00000619888.5	c.73+2358G>A		intron_variant		1	NM_001001991.3	P1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31203 AN: 151950 Hom.: 3503 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.205 AC: 31222 AN: 152068 Hom.: 3505 Cov.: 32 AF XY: 0.203 AC XY: 15090 AN XY: 74338

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.195

Alfa AF: 0.233 Hom.: 2139

Bravo AF: 0.195

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.58

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: rs17727535; hg19: chr11-35544703;