chr11-35523155-C-T

Variant names:

• chr11-35523155-C-T
• rs17727535
• NM_001001991.3:c.73+2358G>A

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001991.3. 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
	PAMR1	NM_001001991.3	MANE Select	c.73+2358G>A		intron	N/A	NP_001001991.1
	PAMR1	NM_015430.4		c.73+2358G>A		intron	N/A	NP_056245.2
	PAMR1	NM_001282675.2		c.-155+5797G>A		intron	N/A	NP_001269604.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAMR1	ENST00000619888.5	TSL:1 MANE Select	c.73+2358G>A		intron	N/A	ENSP00000483703.1
	PAMR1	ENST00000622144.4	TSL:1	c.73+2358G>A		intron	N/A	ENSP00000482899.1
	PAMR1	ENST00000621476.4	TSL:2	c.-155+5797G>A		intron	N/A	ENSP00000480961.1

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

African (AFR) AF: 0.151 AC: 6252 AN: 41492

American (AMR) AF: 0.176 AC: 2694 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3462

East Asian (EAS) AF: 0.0297 AC: 154 AN: 5180

South Asian (SAS) AF: 0.194 AC: 931 AN: 4800

European-Finnish (FIN) AF: 0.279 AC: 2941 AN: 10560

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

European-Non Finnish (NFE) AF: 0.248 AC: 16853 AN: 67974

Other (OTH) AF: 0.195 AC: 412 AN: 2110

Alfa AF: 0.232 Hom.: 2371

Bravo AF: 0.195

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.44
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: rs17727535; hg19: chr11-35544703;