11-35517721-T-C

Variant names:

• chr11-35517721-T-C
• rs650950
• NM_001001991.3:c.73+7792A>G

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+7792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,132 control chromosomes in the GnomAD database, including 31,692 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 0.63 (31692 hom., cov: 33)
• Consequence: PAMR1 NM_001001991.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAMR1	NM_001001991.3	MANE Select	c.73+7792A>G		intron	N/A	NP_001001991.1	Q6UXH9-1
	PAMR1	NM_015430.4		c.73+7792A>G		intron	N/A	NP_056245.2	Q6UXH9-2
	PAMR1	NM_001282675.2		c.-154-4244A>G		intron	N/A	NP_001269604.1	A0A087WXE9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAMR1	ENST00000619888.5	TSL:1 MANE Select	c.73+7792A>G		intron	N/A	ENSP00000483703.1	Q6UXH9-1
	PAMR1	ENST00000622144.4	TSL:1	c.73+7792A>G		intron	N/A	ENSP00000482899.1	Q6UXH9-2
	PAMR1	ENST00000953162.1		c.73+7792A>G		intron	N/A	ENSP00000623221.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95861 AN: 152014 Hom.: 31640 Cov.: 33

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.631 AC: 95973 AN: 152132 Hom.: 31692 Cov.: 33 AF XY: 0.635 AC XY: 47204 AN XY: 74336

African (AFR) AF: 0.787 AC: 32685 AN: 41528

American (AMR) AF: 0.647 AC: 9893 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3470

East Asian (EAS) AF: 0.972 AC: 5034 AN: 5178

South Asian (SAS) AF: 0.725 AC: 3488 AN: 4814

European-Finnish (FIN) AF: 0.507 AC: 5350 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35994 AN: 67976

Other (OTH) AF: 0.594 AC: 1257 AN: 2116

Alfa AF: 0.567 Hom.: 94207

Bravo AF: 0.647

Asia WGS AF: 0.821 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.78
PhyloP100		-1.4
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: rs650950; hg19: chr11-35539269;